Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, non-visual light effects, to bacterial light sensing and harvesting. Light driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond together with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

中文翻译：

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细菌视紫红质中视网膜的光致异构化取样

受限蛋白质袋内的类视黄醇的光异构化代表了从动物视觉、非视觉光效应到细菌光感应和收获的许多重要生物过程中的关键化学事件。细菌视紫红质中的光驱动质子泵浦在其光循环期间需要精细的电子和构象重新配置。然而，当不同的中间体群体共存并随时间演变时，从嘈杂的电子密度图中描绘视网膜光异构化前后的瞬态分子事件一直是一项重大挑战。在这里，我报告了从时间分辨系列晶体学中最近观察到的混合物中解卷积的几种不同的早期光产物。反式视黄醛在进入生产性 13-顺式构型之前经过广泛的异构化取样。光吸收后，发色团尝试在每个双键上进行反式到顺式异构化以及停滞的反式到顺式沿其多烯链在多个单键处旋转。这种异构化采样推动所有七个跨膜螺旋向外弯曲，导致视网膜结合袋的瞬时扩张，随后由于回缩而收缩。在原子分辨率下观察到的这些超快响应支持细菌视紫红质中的生产性光反应是由假体发色团中的光诱导电荷分离引发的，但受其蛋白质袋的立体选择性控制。从混合观测中对同时发生的事件进行数值解析的方法也普遍适用。