FTIR spectroscopy shows weak symmetric hydrogen bonding of the Q_B carbonyl groups in Rhodobacter sphaeroides R26 reaction centres

Bio-organic Synthesi

Asymmetric binding of the 1- and 4-C=0 of QA in Rhodobacter sphaeroides R26 reaction centres monitored by Fourier transform infra-red spectroscopy using site-specific isotopically laballed ubiquinone-10

Solid state NMR/Biophysical Organic Chemistr

Identification of the first steps in charge separation in bacterial photosynthetic reaction centers of Rhodobacter sphaeroides by ultrafast mid-infrared spectroscopy: Electron transfer and protein dynamics

AbstractTime-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy in the region between 1600 and 1800cm−1 was used to investigate electron transfer, radical pair relaxation, and protein relaxation at room temperature in the Rhodobacter sphaeroides reaction center (RC). Wild-type RCs both with and without the quinone electron acceptor QA, were excited at 600nm (nonselective excitation), 800nm (direct excitation of the monomeric bacteriochlorophyll (BChl) cofactors), and 860nm (direct excitation of the dimer of primary donor (P) BChls (PL/PM)). The region between 1600 and 1800cm−1 encompasses absorption changes associated with carbonyl (CO) stretch vibrational modes of the cofactors and protein. After photoexcitation of the RC the primary electron donor P excited singlet state (P*) decayed on a timescale of 3.7ps to the state P+BL− (where BL is the accessory BChl electron acceptor). This is the first report of the mid-IR absorption spectrum of P+BL−; the difference spectrum indicates that the 9-keto CO stretch of BL is located around 1670–1680cm−1. After subsequent electron transfer to the bacteriopheophytin HL in ∼1ps, the state P+HL− was formed. A sequential analysis and simultaneous target analysis of the data showed a relaxation of the P+HL− radical pair on the ∼20ps timescale, accompanied by a change in the relative ratio of the PL+ and PM+ bands and by a minor change in the band amplitude at 1640cm−1 that may be tentatively ascribed to the response of an amide CO to the radical pair formation. We conclude that the drop in free energy associated with the relaxation of P+HL−, is due to an increased localization of the electron hole on the PL half of the dimer and a further consequence is a reduction in the electrical field causing the Stark shift of one or more amide CO oscillators

Effects of the Cryptochrome CryB from Rhodobacter sphaeroides on Global Gene Expression in the Dark or Blue Light or in the Presence of Singlet Oxygen

Several regulators are controlling the formation of the photosynthetic apparatus in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. Among the proteins affecting photosynthesis gene expression is the blue light photoreceptor cryptochrome CryB. This study addresses the effect of CryB on global gene expression. The data reveal that CryB does not only influence photosynthesis gene expression but also genes for the non-photosynthetic energy metabolism like citric acid cycle and oxidative phosphorylation. In addition several genes involved in RNA processing and in transcriptional regulation are affected by a cryB deletion. Although CryB was shown to undergo a photocycle it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress conditions. While there is a large overlap in these responses, some CryB-dependent effects are specific for blue-light or photooxidative stress. In addition to protein-coding genes some genes for sRNAs show CryB-dependent expression. These findings give new insight into the function of bacterial cryptochromes and demonstrate for the first time a function in the oxidative stress response

Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone

Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations

Circadian oscillator proteins across the kingdoms of life : Structural aspects 06 Biological Sciences 0601 Biochemistry and Cell Biology

Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms and control numerous biological processes in a range of organisms. These periodic rhythms are the result of a complex interplay of interactions among clock components. These components are specific to the organism but share molecular mechanisms that are similar across kingdoms. The elucidation of clock mechanisms in different kingdoms has recently started to attain the level of structural interpretation. A full understanding of these molecular processes requires detailed knowledge, not only of the biochemical and biophysical properties of clock proteins and their interactions, but also the three-dimensional structure of clockwork components. Posttranslational modifications (such as phosphorylation) and protein-protein interactions, have become a central focus of recent research, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. The three-dimensional structures for the cyanobacterial clock components are well understood, and progress is underway to comprehend the mechanistic details. However, structural recognition of the eukaryotic clock has just begun. This review serves as a primer as the clock communities move towards the exciting realm of structural biology

Biological sensors: More than one way to sense oxygen

International audienceRecently determined structures of the oxygen-sensing heme domain of the bacterial protein FixL have revealed a new binding environment and signal transduction mechanism for heme; they have also provided new insights into the diverse 'PAS' domain superfamily