Yigal Lahav
Ofer M. Shir
ABSTRACT
Simple optical spectroscopy measurements, namely circular dichroism (CD) and absorption spectra of interacting pigments, can be used for deriving details of their molecular geometry. Unlike X-ray crystallography and NMR that provide highly detailed structural information but consume time and resources, optical spectroscopic measurements that provide valuable information on local interactions are fast, and easy to perform. Unfortunately, structural information may be extracted from optical spectra only upon solving an ill-defined inverse-problem (spectrum → structure). In this paper, we present a computational approach for addressing this problem, relying on simulation-based optimization. We introduce quantum theoretical simulations of both CD and absorption spectra of interacting chlorophylls, integrated with an effective graphical user interface to facilitate an expert's estimation of the chlorophyll geometry. The inverse-problem is then efficiently solved by decomposing it into two approximately independent subproblems and employing two different derandomized Evolution Strategies, while relying on the expert's initial search-point. Our approach is implemented for deriving the geometry of interacting chlorophylls incorporated within natural proteins. It is then demonstrated to retrieve chlorophyll geometries with low errors when compared to the respective geometries determined to near-atomic resolution by X-ray crystallography. The observations are reported and investigated in the light of non-uniqueness and uncertainty.
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Index Terms
- Solving structures of pigment-protein complexes as inverse optimization problems using decomposition
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