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相关概念视频

Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

4.0K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
 
Most enzymes...
4.0K
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

8.3K
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...
8.3K
Enzyme Kinetics01:19

Enzyme Kinetics

97.2K
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...
97.2K
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

20.2K
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...
20.2K
Operon Model01:23

Operon Model

35
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
35
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.8K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Updated: Jul 18, 2025

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening
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Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

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EnzyHTP计算定向进化与自适应性资源配置

Qianzhen Shao1, Yaoyukun Jiang1, Zhongyue J Yang1,2,3,4,5

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.

Journal of chemical information and modeling
|August 23, 2023
PubMed
概括
此摘要是机器生成的。

我们开发了一个计算定向进化协议,使用自适应性资源分配来提高酶工程效率. 这种方法显著降低了计算成本,并成功识别了有益的酶变体.

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Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening
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Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

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A New Screening Method for the Directed Evolution of Thermostable Bacteriolytic Enzymes
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A New Screening Method for the Directed Evolution of Thermostable Bacteriolytic Enzymes

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科学领域:

  • 生物化学 生物化学
  • 计算生物学 计算生物学
  • 酵素工程是什么意思 酵素工程

背景情况:

  • 定向进化对于酶工程至关重要,但依赖于高效的选.
  • 发展 发展 发展 发展
  • 智能图书馆是一个智能图书馆.
  • 识别有益的酶变异仍然是一个挑战.

研究的目的:

  • 开发一种新的计算定向进化协议.
  • 通过适应性资源分配来提高选效率.
  • 验证该协议在识别有益的酶变体方面的有效性.

主要方法:

  • 使用Python库实现适应性资源分配策略,用于酶建模.
  • 使用EnzyHTP软件进行自动化酶建模.
  • 使用酸脱酶和肯普消除酶 (KE07) 测试了该协议.
  • 采用分子动力学 (MD) 和量子力学 (QM) 计算来进行变异分析.

主要成果:

  • 与固定配置相比,自适应资源分配节省了87%的CPU时间和14%的GPU时间.
  • 该协议成功地确定了Kemp消除酶 (KE07) 的四种实验观察到的目标变异.
  • 计算任务,包括18.4μs MD和18,400 QM计算,在3天内完成.

结论:

  • 开发的具有适应性资源分配的计算定向进化协议提高了效率并降低了成本.
  • 这种方法有效地识别了有益的酶变体,帮助了酶工程的努力.
  • 该协议在计算酶设计方面取得了重大进展.