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PLMC:蛋白质序列的语言模型 增强蛋白质结晶预测
Dapeng Xiong1,2, Kaicheng U3, Jianfeng Sun4
1Department of Computational Biology, Cornell University, Ithaca, 14853, USA. dx38@cornell.edu.
Interdisciplinary sciences, computational life sciences
|August 18, 2024
概括
我们开发了PLMC,这是一个深度学习框架,用于预测蛋白质结晶倾向. 该工具提高了多阶段预测的准确性,帮助研究人员更有效地设计可结晶的蛋白质变体.
科学领域:
- 结构生物学 结构生物学
- 计算生物学 计算生物学
- 生物物理学的生物物理.
背景情况:
- 射线衍射晶体学是确定蛋白质3D结构的关键方法,但需要可结晶的蛋白质.
- 蛋白质结晶是一个复杂的,多阶段的过程 (生产,净化,晶体生长) 是昂贵和劳动密集的.
- 需要预测计算工具来指导通过估计蛋白质结晶倾向的实验努力.
研究的目的:
- 引入PLMC,这是一种新的深度学习框架,旨在增强多阶段蛋白质结晶倾向的预测.
- 利用预先训练的蛋白质语言模型,并整合各种功能集,以提高预测准确度.
- 帮助研究人员优化实验设计,以获得可结晶的蛋白质变体.
主要方法:
- 开发了一个深度学习框架 (PLMC),集成了一个预先训练的蛋白质语言模型.
- 组合蛋白质语言嵌入与手工制作的特征 (物理化学,基于序列,与失序相关的).
- 采用单独的嵌入和连接策略来进行特征改进和最终预测.
主要成果:
- PLMC获得了高AUC得分:0.773 (第一阶段1),0.893 (第二阶段),0.913 (第三阶段) 和0.982 (最终结晶).
- 与现有的最先进的方法相比,在所有预测阶段都表现出卓越的性能.
- 对球状蛋白和膜蛋白都显示出极高的准确性,膜蛋白的AUC为0.991.
结论:
- PLMC显著改善了跨多个阶段的蛋白质结晶倾向的预测.
- 该框架能够整合多样化的功能,并利用预先训练的模型提供了一个强大的新工具.
- 在加快和优化实验性蛋白质结晶工作流程方面,PLMC具有巨大的潜力.
相关概念视频
Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
Globular and Fibrous Proteins
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Nucleic Acid Structure
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
DNA Structure
DNA has a double-helix structure. The...

