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相关概念视频

Enzyme Kinetics01:19

Enzyme Kinetics

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Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
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Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

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Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Determination of Michaelis Constant and Maximum Elimination Rate01:20

Determination of Michaelis Constant and Maximum Elimination Rate

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The Michaelis constant (KM) and the theoretical maximum process rate (Vmax) are vital parameters in the Michaelis-Menten equation, central to many biochemical reactions. They provide essential insights into enzyme kinetics and drug metabolism.
These parameters can be estimated by analyzing plasma concentration data post-drug administration. A notable example of this application is phenytoin, a drug with capacity-limited kinetics. It's recommended that phenytoin should be administered at two...
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Measuring Reaction Rates03:09

Measuring Reaction Rates

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Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical...
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相关实验视频

Updated: Jun 6, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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使用可转移数据驱动的集体变量对不同基质的酶活性进行关联.

Sudip Das1, Umberto Raucci1, Rui P P Neves2

  • 1Atomistic Simulation Research Line, Italian Institute of Technology, Genova GE 16152, Italy.

Proceedings of the National Academy of Sciences of the United States of America
|November 26, 2024
PubMed
概括
此摘要是机器生成的。

机器学习识别了用于药物发现的酶反应性构造. 这种方法加速了对酶催化物的理解,并评估了针对II型糖尿病等疾病的新抑制剂.

关键词:
活动地点和基板预组织活动.酶催化酶的催化作用葡萄糖溶解是什么基于机器学习的集体变量.转移学习转移学习

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Defining Substrate Specificities for Lipase and Phospholipase Candidates
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相关实验视频

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Defining Substrate Specificities for Lipase and Phospholipase Candidates
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Collecting Variable-concentration Isothermal Titration Calorimetry Datasets in Order to Determine Binding Mechanisms
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科学领域:

  • 生物化学 生化学
  • 计算生物学 计算生物学
  • 酶学 是一种酶学.

背景情况:

  • 识别酶基质反应性构造对于理解催化作用至关重要.
  • 由于复杂的自由能源景观,传统方法面临挑战.
  • 人类胰腺α-氨酶是治疗II型糖尿病的关键酶.

研究的目的:

  • 应用机器学习 (ML) 技术来识别酶反应性构造 (RC).
  • 为了将基于ML的集体变量 (CV) 与实验催化活性相关联.
  • 为了简化酵素过程的计算建模.

主要方法:

  • 利用基于ML的集体变量 (CV) 来建模酶基质相互作用.
  • 专注于人类胰腺α-氨酶和马尔托-寡糖糖基质.
  • 与在RC中的概率与实验催化活性相关联.

主要成果:

  • 开发了基于ML的CV,可以准确预测反应性构造.
  • 证明了这些CV在不同的基板上具有显著的可转移性.
  • 显著减少了对模拟的计算需求和手动干预.

结论:

  • ML提供了一种有效的方法来识别酶反应性构造.
  • 这种方法促进了对酶催化物的理解.
  • 这种方法有可能加速药物发现和抑制剂开发.