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相关概念视频

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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用描述器增强的机器学习来预测酶化学相互作用.

Yilei Han1, Haoye Zhang2, Zheni Zeng2

  • 1Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.

Synthetic and systems biotechnology
|March 7, 2024
PubMed
概括

蛋白质描述器提高了对新型酶的酶活性预测,而化学描述器有助于预测新的化学活动. 在与酶相关的任务中,ESM-2蛋白质描述器表现最好.

关键词:
描述器描述器是一个描述器.酶设计 酶设计酶-基质相互作用机器学习 机器学习

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科学领域:

  • 计算生物学和化学信息学
  • 酶工程和设计与设计

背景情况:

  • 描述器对于在酶设计中对酶和化学物质进行表征至关重要,以实现可持续的生化合成.
  • 了解酶化学关系是推动生物化学生产的关键.
  • 机器学习模型需要有效的描述器来准确预测.

研究的目的:

  • 评估各种蛋白质和化学描述剂对随机森林模型性能对酶化学关系预测的影响.
  • 通过三个情景来评估描述者的影响:新的关系,新的酶和新的化学评估.
  • 为开发针对特定酶家族量身定制的机器学习模型提供指导.

主要方法:

  • 来自现有文献的七个酶家族的精选酶活性数据.
  • 开发了一个机器学习管道,使用10倍交叉验证来评估模型性能.
  • 评估了蛋白质 (基于序列和基于结构,包括esm-2) 和化学描述符,用于预测已知/新兴酶和化学物质的酶活性.

主要成果:

  • 在大多数数据集中,蛋白质描述器显著改善了用于新酶评估的模型性能,esm-2描述器产生了最佳结果.
  • 化学描述符对新的酶评估没有影响,但在几个数据集中显著改善了新的化学评估.
  • 数据集特征,如序列相似性和大小,与模型性能和描述器实用性相关联.

结论:

  • 描述物的选择至关重要,并且取决于具体的预测任务 (新酶与新化学物质).
  • 蛋白质描述器,特别是esm-2,对于预测新型酶活动非常有价值.
  • 化学描述符更有效地预测新化学物质对已知的酶的活性,指导未来的酶设计和发现.