Du Siyuan, Kretsch Rachael C, Parres-Gold Jacob, Pieri Elisa, Cruzeiro Vinícius Wilian D, Zhu Mingning, Pinney Margaux M, Yabukarski Filip, Schwans Jason P, Martínez Todd J, Herschlag Daniel
Department of Biochemistry, Stanford University, Stanford, CA, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Science. 2025 Jan 2;387(6735):eado5068. doi: 10.1126/science.ado5068. Epub 2025 Feb 14.
Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. Our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.
酶以多种状态的集合形式存在，这些状态编码了其催化作用背后的能量学。由17种丝氨酸蛋白酶的1231个结构构建的构象集合揭示了它们反应状态下的原子水平变化。通过比较酶促反应和溶液反应，我们确定了提供催化作用的分子特征，并量化了它们对催化作用的能量贡献。丝氨酸蛋白酶将其反应物精确地定位在不稳定的构象中，形成一个能量下坡梯度，该梯度选择性地有利于反应所需的运动，同时限制非反应途径的构象状态。相同的催化特征在多种不同结构折叠的蛋白酶和其他酶中反复进化。我们的集合功能分析揭示了以前未知的催化特征，提供了基于简单物理和化学原理的定量模型，并确定了自然界中反复出现的基序，这些基序可能会启发酶的设计。
