Search results for "conformation"
showing 10 items of 1414 documents
Reconfigurable DNA Origami Nanocapsule for pH-Controlled Encapsulation and Display of Cargo
2019
DNA nanotechnology provides a toolbox for creating custom and precise nanostructures with nanometer-level accuracy. These nano-objects are often static by nature and serve as versatile templates for assembling various molecular components in a user-defined way. In addition to the static structures, the intrinsic programmability of DNA nanostructures allows the design of dynamic devices that can perform predefined tasks when triggered with external stimuli, such as drug delivery vehicles whose cargo display or release can be triggered with a specified physical or chemical cue in the biological environment. Here, we present a DNA origami nanocapsule that can be loaded with cargo and reversibl…
Molecular phylogeny and ultrastructure of the lichen microalga Asterochloris mediterranea sp. nov. from Mediterranean and Canary Islands ecosystems
2015
The microalgae of the genus Asterochloris are the preferential phycobionts in Cladonia, Lepraria and Stereocaulon lichens. Recent studies have highlighted the hidden diversity of the genus, even though phycobionts hosting Cladonia spp. in Mediterranean and Canarian ecosystems have been poorly explored. Phylogenetic analyses were made by concatenation of the sequences obtained with a plastid -LSU rDNA- and two nuclear -ITS rDNA and actin- molecular markers of the phycobionts living in several populations of Cladonia convoluta-C. foliacea complex, C. rangiformis and C. cervicornis species widely distributed in these areas in a great variety of substrata and habitats. A new strongly supported …
Tuning the Electrochemistry of Free-Base Porphyrins in Acidic Nonaqueous Media: Influence of Solvent, Supporting Electrolyte, and Ring Substituents
2016
International audience; A detailed study of reduction potentials, electroreduction mechanisms and acid-base chemistry was carried out on two series of free-base porphyrins in nonaqueous media. The first series is represented by four-pyrrole substituted tetraphenylporphyrin (TPP) derivatives, two of which are planar and two of which are nonplanar in their non-protonated form. The second comprises porphyrins with 0-4 meso-phenyl groups on the macrocycle. Equilibrium constants for conversion of each neutral porphyrin to its diprotic [H4P] 2+ form were determined and the electrochemistry was then elucidated as a function of: (i) type of nonaqueous solvent, (ii) anion of supporting electrolyte, …
Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome
2022
Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory …
Inactivation and polymerization of human neuroserpin
2010
Neuroserpin is an inhibitory enzyme, belonging to the family of serpins and involved in several pathologies, such as ischemia, Alzheimer disease, and FENIB (Familial Encephalopathy with Neuroserpin Inclusion Body). Here, we study the mechanism of neuroserpin inactivation and polymerization by different experimental techniques (static and dynamic light scattering, liquid chromatography, Fourier transform infrared spectroscopy, emission spectroscopy). Our results show that at intermediate temperatures (45-55 °C) neuroserpin forms flexible polymers with a size from a few tens to a few hundreds of nanometers. At high temperatures, above 80 °C, our results reveal a different polymeric form, reac…
Nitrated Fatty Acids Modulate the Physical Properties of Model Membranes and the Structure of Transmembrane Proteins
2017
Nitrated fatty acids (NO2 -FAs) act as anti-inflammatory signal mediators, albeit the molecular mechanisms behind NO2 -FAs' influence on diverse metabolic and signaling pathways in inflamed tissues are essentially elusive. Here, we combine fluorescence measurements with surface-specific sum frequency generation vibrational spectroscopy and coarse-grained computer simulations to demonstrate that NO2 -FAs alter lipid organization by accumulation at the membrane-water interface. As the function of membrane proteins strongly depends on both, protein structure as well as membrane properties, we consecutively follow the structural dynamics of an integral membrane protein in presence of NO2 -FAs. …
Light-induced, site-selective isomerization of glyoxylic acid in solid xenon
2014
Abstract The isomerization of glyoxylic acid (GA) and its water complex was studied in a low temperature xenon matrix. The aim of these studies was to understand how xenon environment affects the cis-trans GA interconversion upon near infrared irradiation. In solid xenon, the GA conformers are embedded in two different matrix sites. These show up as different vibrational bands of GA that exhibit different kinetic rates of isomerization. Upon complexation with water, the isomerization process slows down. Xenon matrix appears not to affect energy relaxation process via intramolecular or intermolecular hydrogen bond as compared with previous experiments in an argon.
Dynamic Refolding of Ion-Pair Catalysts in Response to Different Anions.
2019
Four distinct folding patterns were identified in two foldamer-type urea-thiourea catalysts bearing a basic dimethylamino unit by a combination of X-ray crystallography, solution NMR studies, and computational studies (DFT). These patterns are characterized by different intramolecular hydrogen bonding schemes that arise largely from different thiourea conformers. The free base forms of the catalysts are characterized by folds where the intramolecular hydrogen bonds between the urea and the thiourea units remain intact. In contrast, the catalytically relevant salt forms of the catalyst, where the catalyst forms an ion pair with the substrate or substrate analogues, appear in two entirely dif…
Combined NC-AFM and DFT study of the adsorption geometry of trimesic acid on rutile TiO2(110)
2010
The adsorption behavior of trimesic acid (TMA) on rutile TiO(2)(110) is studied by means of non-contact atomic force microscopy (NC-AFM) and density-functional theory (DFT). Upon low-coverage adsorption at room temperature, NC-AFM imaging reveals individual molecules, centered above the surface titanium rows. Based on the NC-AFM results alone it is difficult to deduce whether the molecules are lying flat or standing upright on the surface. To elucidate the detailed adsorption geometry, we perform DFT calculations, considering a large number of different adsorption positions. Our DFT calculations suggest that single TMA molecules adsorb with the benzene ring parallel to the surface plane. In…
Modeling of the N-terminal Section and the Lumenal Loop of Trimeric Light Harvesting Complex II (LHCII) by Using EPR
2015
The major light harvesting complex II (LHCII) of green plants plays a key role in the absorption of sunlight, the regulation of photosynthesis, and in preventing photodamage by excess light. The latter two functions are thought to involve the lumenal loop and the N-terminal domain. Their structure and mobility in an aqueous environment are only partially known. Electron paramagnetic resonance (EPR) has been used to measure the structure of these hydrophilic protein domains in detergent-solubilized LHCII. A new technique is introduced to prepare LHCII trimers in which only one monomer is spin-labeled. These heterogeneous trimers allow to measure intra-molecular distances within one LHCII mon…