scholarly journals Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems

2015 ◽  
Vol 17 (34) ◽  
pp. 22054-22063 ◽  
Author(s):  
Ananya Debnath ◽  
Sabine Wiegand ◽  
Harald Paulsen ◽  
Kurt Kremer ◽  
Christine Peter
Keyword(s):  
Lipid Bilayers ◽  
Light Harvesting ◽  
Simulation Models ◽  
Coarse Grained ◽  
Light Harvesting Complex ◽  
Green Plants ◽  
Coarse Grained Model ◽  
Multi Scale ◽  
Harvesting Systems ◽  
Association Behavior

A coarse-grained model is derived for chlorophyll molecules in lipid bilayers using a multi-scale simulation ansatz aiming to understand the association behavior of the light harvesting complex (LHCII) of green plants.

Multi-scale simulations of biological systems using the OPEP coarse-grained model

2018 ◽  
Vol 498 (2) ◽  
pp. 296-304 ◽  
Author(s):  
Fabio Sterpone ◽  
Sébastien Doutreligne ◽  
Thanh Thuy Tran ◽  
Simone Melchionna ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Biological Systems ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Multi Scale

Effects of Aggregation on Trimeric Light-Harvesting Complex II of Green Plants:  A Hole-Burning Study

1999 ◽  
Vol 103 (14) ◽  
pp. 2422-2428 ◽  
Author(s):  
J. Pieper ◽  
K.-D. Irrgang ◽  
M. Rätsep ◽  
R. Jankowiak ◽  
Th. Schrötter ◽  
...  
Keyword(s):  
Light Harvesting ◽  
Hole Burning ◽  
Light Harvesting Complex ◽  
Green Plants ◽  
Complex Ii ◽  
Light Harvesting Complex Ii

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

scholarly journals Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
pp. e01044-20
Author(s):  
Karel Kopejtka ◽  
Jürgen Tomasch ◽  
Yonghui Zeng ◽  
Vadim Selyanin ◽  
Marko Dachev ◽  
...  
Keyword(s):  
Light Harvesting ◽  
Reaction Centers ◽  
Light Energy ◽  
Natural Environments ◽  
Experimental Conditions ◽  
Light Harvesting Complex ◽  
Rhodopsin Gene ◽  
Harvesting Systems ◽  
Photosynthesis Genes ◽  
High Concentrations

ABSTRACTPhotoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.

Ultrafast chlorophyllb-chlorophyllaexcitation energy transfer in the isolated light harvesting complex, LHC II, of green plants

FEBS Letters ◽  
1994 ◽  
Vol 339 (1-2) ◽  
pp. 134-138 ◽  
Author(s):  
Lars Olof Pålsson ◽  
Michael D. Spangfort ◽  
Vidmantas Gulbinas ◽  
Tomas Gillbro
Keyword(s):  
Energy Transfer ◽  
Light Harvesting ◽  
Lhc Ii ◽  
Light Harvesting Complex ◽  
Green Plants
Sign in / Sign up

Export Citation Format

Share Document