复原阿尔多尔酶的新计算设计
Lin Jiang1, Eric A Althoff, Fernando R Clemente
1Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Science (New York, N.Y.)
|March 8, 2008
概括
计算式蛋白质设计创造了新的逆酶酶,用于催化反应. 使用水分子作为催化剂的设计更成功,其结构通过X射线晶体学得到证实.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 蛋白质工程是指蛋白质工程.
背景情况:
- 酶催化对于生物过程至关重要.
- 设计具有特定功能的新型酶仍然是蛋白质工程中的一个重大挑战.
- 计算式蛋白质设计旨在为所需的化学反应创建酶.
研究的目的:
- 使用计算方法设计新的逆酶酶.
- 在非自然基质中催化碳-碳键的断裂.
- 为了探索酶活性的不同催化动机.
主要方法:
- 利用新的算法与哈希技术来构建多步反应的活性站点.
- 设计的反-阿尔多拉体,包含四种不同的催化基因.
- 实验性地描述了72种设计的酶.
- 确定了活跃设计的X射线晶体结构.
主要成果:
- 在72个设计的反体中,有32个表现出可检测的活动.
- 使用明确的水分子进行质子转移的设计显示出明显更高的成功率.
- 观察到速度加速高达四个数量级,以及多次转机.
- X射线晶体结构证实了计算设计模型的原子精度.
结论:
- 计算式蛋白质设计可以成功地为非自然反应创建功能性酶.
- 对这些酶而言,明确的水介质质子混动是一种比充电侧链网络更有效的催化策略.
- 设计的酶在计算模型和实验结构之间表现出高保真性.
相关概念视频
00:57C–C Bond Cleavage: Retro-Aldol Reaction
The reverse of the aldol addition reaction is called the retro-aldol reaction. Here, the carbon–carbon bond in the aldol product is cleaved under acidic or basic conditions to form two molecules of carbonyl compounds. The mechanism of the reaction consists of three steps.
In the first step, as depicted in Figure 1, the base deprotonates the β-hydroxy ketone at the hydroxyl group to form an alkoxide ion.
In the first step, as depicted in Figure 1, the base deprotonates the β-hydroxy ketone at the hydroxyl group to form an alkoxide ion.
01:08Base-Catalyzed Aldol Addition Reaction
As depicted in Figure 1, base-catalyzed aldol addition involves adding two carbonyl compounds in aqueous sodium hydroxide to form a β-hydroxy carbonyl compound.
01:27Aldol Condensation with β-Diesters: Knoevenagel Condensation
The Knoevenagel condensation is an aldol-type reaction involving the condensation of aldehydes or ketones with active methylene compounds such as β-diesters to produce substituted olefins.
01:10C–C Bond Formation: Aldol Condensation Overview
Aldol condensation is an important route in synthetic organic chemistry used to generate a new carbon–carbon bond under basic or acidic conditions. The aldol condensation reaction presented in Figure 1 constitutes an aldol addition reaction followed by the dehydration process.
01:33Aldol Condensation vs Claisen Condensation
Aldol condensation is an acid or base-catalyzed condensation between aldehydes or ketones to give an α,ꞵ-unsaturated carbonyl compound. A base-promoted condensation between ester molecules to produce a ꞵ-ketoester is known as the Claisen condensation. In the presence of a base, both reactions involve deprotonation of the acidic α hydrogen to produce the corresponding enolates. The nucleophilic enolates attack their respective nonenolized carbonyl compound forming a tetrahedral intermediate.
01:31Diels–Alder vs Retro-Diels–Alder Reaction: Thermodynamic Factors
The Diels–Alder reaction is thermally reversible, meaning that the reaction reverts to the starting diene and dienophile under suitable temperatures. The forward reaction gives a cyclohexene derivative and is favored at low to medium temperatures. The reverse process, also called retro-Diels–Alder reaction, is a ring-opening process favored at high temperatures.