10/11 – Zhong Ren, University of Illinois Chicago
CBQB Seminar
October 11, 2021
12:00 PM - 1:00 PM
Address
Chicago, IL
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Title: Numerical Resolution of Heterogeneity in Protein Structures by Singular Value Decomposition
Abstract: Singular value decomposition (SVD) and the subsequent Ren rotation in the multi-dimensional Euclidian space established by SVD have been incrementally developed in the recent years to resolve simultaneous signals mixed in the characterization of structural dynamics of proteins. I will present several case studies to demonstrate why structural signals due to different origins often coexist in datasets of dynamic crystallography. Structural interpretation could be severely hindered by mixed signals if not properly unscrambled. An analytical strategy of decomposition and deconvolution has been applied to solve several problems in structural biology. This method for a numerical resolution of concurrent chemical events from mixed observations is generally applicable. One of the most recent studies is the finding of solid evidence to support isomerization sampling of retinal in bacteriorhodopsin upon photoexcitation. 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. 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. SVD analysis 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. 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 (Ren, bioRxiv doi:10.1101/2021.09.16.460656, 2021).
Date posted
Oct 6, 2021
Date updated
Oct 6, 2021