Multiscale computational studies of biological light capture

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http://urn.fi/URN:ISBN:978-951-51-4094-4
Title: Multiscale computational studies of biological light capture
Author: Suomivuori, Carl-Mikael
Contributor: University of Helsinki, Faculty of Science, Department of Chemistry, Molecular science
Technical University of Munich, Germany
Thesis level: Doctoral dissertation (article-based)
Abstract: The efficient absorption and utilization of sunlight is one of the most fundamental processes of life, as it is required both for photosynthesis and for visual perception. Biological light capture occurs through light-sensitive molecules called chromophores, which are embedded in complex protein environments that greatly affect both the wavelength of the absorbed light and the subsequent light-triggered activation process. Despite extensive experimental and theoretical studies of photobiological systems, the molecular mechanisms by which proteins affect the light absorption of biological chromophores remain unclear. In this doctoral thesis, we combine large-scale correlated quantum chemical calculations, hybrid quantum mechanics/molecular mechanics (QM/MM) methods, and extensive classical molecular dynamics (MD) simulations to address the light capture in photobiological systems. We employ these computational approaches to study the green fluorescent protein (GFP), photosynthetic reaction centers, as well as both artificial and natural retinylidene proteins. We show how correlated second-order ab initio calculations can be made feasible for large quantum chemical models by employing the reduced virtual space (RVS) and Laplace-transformed scaled opposite-spin (LT-SOS) approximations. Our results uncover intrinsic differences in the excited-state properties of different photosynthetic reaction centers and help determine the color-tuning mechanism of retinal in engineered rhodopsin mimics. Finally, as a result of this work, we propose a mechanism for the ion translocation in the newly discovered light-driven Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2). Elucidating the fundamental physical and chemical principles behind biological light capture is essential for developing, e.g., novel biomarkers, optogenetic tools, and biomimetic catalysts for energy conversion.Att fånga och utnyttja solljus är en av livets mest centrala processer, eftersom det möjliggör både fotosyntes samt ger förmågan att förnimma ljus och färger. Fotobiologiska system absorberar fotoner med hjälp av ljuskänsliga molekyler som är inbäddade i komplexa proteinomgivningar. Proteinerna påverkar i sin tur både våglängden av det upptagna ljuset samt hur ljusenergin omvandlas till användbar form. Det inte klart hur ljusaktiveringen hos fotobiologiska system sker på molekylnivån, trots att man har studerat fenomenet i flera årtionden. I denna avhandling utnyttjar vi toppmodern beräkningskemisk metodologi för att utreda hur ljusinfångningen sker hos grönt fluorescerande protein (GFP), olika fotosyntetiska reaktionscentra samt retinalbindande proteiner. Våra beräkningar ger insikt om hur elektronstrukturen skiljer sig åt mellan reaktionscentra hos olika fotosyntetiska system samt hur proteinomgivningar påverkar färgen av det absorberade ljuset hos retinalbindande proteiner. Vi föreslår även en mekanism för hur joner transporteras av en nyligen identifierad ljusdriven natriumpump, Krokinobacter eikastus rodopsin 2 (KR2). Att förstå de grundläggande fysikaliska och kemiska principerna bakom biologisk ljusinfångning är väsentligt för att kunna utveckla nya neurofysiologiska verktyg samt ny solbaserad energiteknologi.
URI: URN:ISBN:978-951-51-4094-4
http://hdl.handle.net/10138/232238
Date: 2018-03-02
Subject:
Rights: This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.


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