novoStoic2.0:用于途径合成,热力学评估和酶选择的综合框架
Vikas Upadhyay1, Mohit Anand1, Costas D Maranas1
1Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
PLoS computational biology
|August 6, 2025
概括
novoStoic2.0简化了生物技术的计算路径设计. 这个平台整合了固体测量,de novo路径设计,热力学可行性和用于可持续生物生产的酶选择.
科学领域:
- 合成生物学 合成生物学
- 代谢工程是代谢工程.
- 生物化学工程是生物化学工程.
背景情况:
- 计算路径设计对于开发新的生化生产路径和生物降解策略至关重要.
- 有效的路径设计需要对生物化学,酶动力学和热力学原理有深入的了解.
- 现有的方法往往缺乏整合,阻碍了有效和可行的代谢途径的设计.
研究的目的:
- 推出novoStoic2.0,这是一个集成的计算平台,用于设计和优化生物化学途径.
- 为路径设计,热力学评估和酶选择提供统一的基于Web的界面.
- 通过简化路径工程来促进可持续生物技术解决方案的开发.
主要方法:
- novoStoic2.0集成了用于估计静脉测量,设计新合成途径和评估热力学可行性的工具.
- 该平台包含一个酶选择模块,用于重新设计新的反应步骤.
- 在AlphaSynthesis平台 (http://novostoic.platform.moleculemaker.org/) 内的基于Web的接口可以访问这些工具.
主要成果:
- novoStoic2.0可以设计热力学可行的代谢途径.
- 该平台有助于选择合适的酶用于途径的构建和优化.
- 在识别具有减少辅因子要求的新型,较短的氧铁醇合成途径方面已证明有用.
结论:
- novoStoic2.0显著简化了计算路径设计的过程.
- 该平台支持开发创新和可持续的生物技术应用.
- 通过整合关键设计步骤,novoStoic2.0加速了新生物生产路线的工程.
相关概念视频
02:55Synthetic Biology
5.0K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
5.0K
01:29Amino Acid Biosynthetic Pathways
138
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
138
01:19Introduction to Enzyme Kinetics
20.8K
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...
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...
20.8K
01:19Enzyme Kinetics
98.8K
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...
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...
98.8K
01:06Thermodynamic Systems
5.4K
A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
Consider an example of tea boiling in a kettle. The...
Consider an example of tea boiling in a kettle. The...
5.4K
02:31Multi-Step Reactions
7.5K
Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
7.5K