计算管道揭示了大自然未开发的化酶储备
bioRxiv : the preprint server for biology
|February 6, 2026
概括
我们开发了一个数据库和计算管道,以精确识别微生物基因组中的化酶. 这有助于发现具有潜在生物医学应用的新化天然产品.
科学领域:
- 生物化学 生物化学
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
背景情况:
- 微生物化天然产品 (hNPs) 在生态和生物医学上具有重要意义.
- 准确识别生物合成酶,特别是基酶,对于预测hNP潜力至关重要.
- 基因组和元基因组数据往往缺乏详细的原酶注释.
研究的目的:
- 为了创建一个手动策划的基酶数据库.
- 开发一条计算管道,用于精确的酶注释.
- 改善微生物hNPs的发现和预测.
主要方法:
- 手动化超过120个经过实验验证或在中推断出的化物.
- 使用催化残留物,保存动机和隐藏的马尔科夫模型 (pHMMs) 进行计算管道的开发.
- 使用序列相似性网络 (SSN) 进行分析,以识别尚未探索的酶集群.
主要成果:
- 一个全面的数据库 (https://halogenases.secondarymetabolites.org/) 详细介绍了化物特异性,催化残留物和突变发生的数据.
- 一个验证的计算管道为家族,基质和化物范围注释的化酶.
- 鉴定了一种具有独特化物偏好的新型化酶 (Rhoba VHPO).
结论:
- 数据库和工作流提供可扩展的解决方案,用于基因组数据中系统的酶注释.
- 改善基酶的分类提高了对微生物hNP结构的预测.
- 这项工作支持生态评估,并加速自然产品的发现.
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相关概念视频
Halogenation of Alkenes
Halogenation is the addition of chlorine or bromine across the double bond in an alkene to yield a vicinal dihalide. The reaction occurs in the presence of inert and non-nucleophilic solvents, such as methylene chloride, chloroform, or carbon tetrachloride.
Consider the bromination of cyclopentene. Molecular bromine is polarized in the proximity of the π electrons of cyclopentene. An electrophilic bromine atom adds across the double bond, forming a cyclic bromonium ion intermediate.
Consider the bromination of cyclopentene. Molecular bromine is polarized in the proximity of the π electrons of cyclopentene. An electrophilic bromine atom adds across the double bond, forming a cyclic bromonium ion intermediate.
Formation of Halohydrin from Alkenes
An alkene, such as propene, reacts with bromine in the presence of water to yield a halohydrin. Halohydrins contain a halogen and a hydroxyl group attached to adjacent carbons. When the halogen is bromine, it is called a bromohydrin, while a chlorohydrin has chlorine as the halogen.
Electrophilic Addition to Alkynes: Hydrohalogenation
Electrophilic addition of hydrogen halides, HX (X = Cl, Br or I) to alkenes forms alkyl halides as per Markovnikov's rule, where the hydrogen gets added to the less substituted carbon of the double bond. Hydrohalogenation of alkynes takes place in a similar manner, with the first addition of HX forming a vinyl halide and the second giving a geminal dihalide.
Base-Promoted α-Halogenation of Aldehydes and Ketones
α-Halogenation of aldehydes and ketones is a reaction involving the substitution of α hydrogens with halogens in the presence of a base. The reaction begins with the abstraction of α hydrogen by the base to produce a nucleophilic enolate ion. This intermediate undergoes a subsequent nucleophilic substitution with the halogen to produce a monohalogenated carbonyl compound. If the starting substrate has more than one α hydrogen, it is difficult to stop the reaction at the stage of...
Radical Substitution: Halogenation of Alkanes and Alkyl Substituents
In the presence of heat or light, alkanes react with molecular halogens to form alkyl halides by a substitution reaction called radical halogenation. This reaction has three steps: initiation, propagation, and termination, as seen in the radical chlorination of methane to produce methyl chloride.
In the initiation step of the reaction, the chlorine molecule undergoes homolytic cleavage in the presence of light or heat, forming two highly reactive chlorine radicals. Propagation occurs in two...
In the initiation step of the reaction, the chlorine molecule undergoes homolytic cleavage in the presence of light or heat, forming two highly reactive chlorine radicals. Propagation occurs in two...
Radical Halogenation: Thermodynamics
The thermodynamic favorability of a reaction is determined by the change in Gibbs free energy (ΔG). ΔG has two components- enthalpy (ΔH) and entropy (ΔS). The entropy component is negligible for alkane halogenation because the number of reactants and product molecules are equal. In this case, the ΔG is governed only by the enthalpy component. The most crucial factor that determines ΔH is the strength of the bonds. ΔH can be determined by comparing the energy between bonds broken and bonds...
