深度转移学习用于跨膜蛋白质复合体的链际接触预测
Peicong Lin1, Yumeng Yan1, Huanyu Tao1
1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
Nature communications
|August 15, 2023
概括
DeepTMP是一种新的深度转移学习方法,可以准确地预测跨膜蛋白质复合体中的链际接触. 它利用来自非跨膜蛋白的预先训练的知识,提高了膜蛋白结构预测的准确性和稳定性.
科学领域:
- 生物化学和结构生物学
- 计算生物学和生物信息学
- 基因组学和蛋白质组学
背景情况:
- 膜蛋白占人类基因的25%,对细胞功能至关重要.
- 准确预测链间残留物-残留物接触对于理解膜蛋白复杂结构和机制至关重要.
- 由于数据有限,现有的深度学习方法在跨膜蛋白质的链际接触预测方面扎.
研究的目的:
- 开发一种深度转移学习方法,DeepTMP,用于准确预测跨膜蛋白质复合体中的链际接触.
- 通过利用非跨膜蛋白的知识来解决对跨膜蛋白的有限数据的挑战.
- 提高对膜蛋白复杂结构和分子机制的理解.
主要方法:
- 开发了DeepTMP,一种深度转移学习方法,利用从非跨膜蛋白中预先训练的知识.
- 整合了一个几何三角感知模块,以捕捉从共同进化的信息中产生的链间相互作用.
- 使用先进的蛋白质语言模型生成共进化的信息.
主要成果:
- DeepTMP显著提高了跨膜蛋白质复合体链间接触预测的精度.
- 该方法在52个自我关联的跨膜蛋白质复合物的数据集上进行了广泛的评估.
- 在准确性和稳定性方面,DeepTMP超过了DeepHomo2.0,CDPred,GLINTER,DeepHomo和DNCON2_Inter等最先进的方法.
结论:
- 在预测跨膜蛋白质复合体的链间接触方面,DeepTMP代表了重大进展.
- 转移学习方法有效地克服了跨膜蛋白研究中的数据限制.
- 这种方法提高了膜蛋白结构预测和机理学研究的准确性和稳定性.
相关概念视频
Multi-pass Transmembrane Proteins and β-barrels
5.3K
In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
5.3K
Single-pass Transmembrane Proteins
5.0K
Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
5.0K
Protein Translocation Machinery on the ER Membrane
4.7K
The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
4.7K
Insertion of Multi-pass Transmembrane Proteins in the RER
8.1K
The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
8.1K
Protein Transport into the Inner Mitochondrial Membrane
3.7K
Nuclear encoded mitochondrial precursors are imported to the inner membrane in a multistep process involving two separate translocons, TIM22 and TIM23. TIM23 is a cation-selective pore that remains closed by the N terminal segment of the protein. Negative charges on the TIM23 act as a receptor for the incoming precursor, pulling the positively charged matrix-targeting sequence for peptide insertion and translocation.
Transport of mitochondrial precursors across the TIM23 channel is driven by...
Transport of mitochondrial precursors across the TIM23 channel is driven by...
3.7K
Protein Complexes with Interchangeable Parts
1.9K
1.9K


