The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation

Atlastin (ATL) GTPases catalyze homotypic membrane fusion of the peripheral endoplasmic reticulum (ER). GTP-hydrolysis–driven conformational changes and membrane tethering are prerequisites for proper membrane fusion. However, the molecular basis for regulation of these processes is poorly understood. Here we establish intrinsic and extrinsic modes of ATL1 regulation that involve the N-terminal hypervariable region (HVR) of ATLs. Crystal structures of ATL1 and ATL3 exhibit the HVR as a distinct, isoform-specific structural feature. Characterizing the functional role of ATL1’s HVR uncovered its positive effect on membrane tethering and on ATL1’s cellular function. The HVR is post-translationally regulated through phosphorylation-dependent modification. A kinase screen identified candidates that modify the HVR site specifically, corresponding to the modifications on ATL1 detected in cells. This work reveals how the HVR contributes to efficient and potentially regulated activity of ATLs, laying the foundation for the identification of cellular effectors of ATL-mediated membrane processes.

Glycosaminoglycan-Based Cryogels as Scaffolds for Cell Cultivation and Tissue Regeneration

Cryogels are a class of macroporous, interconnective hydrogels polymerized at sub-zero temperatures forming mechanically robust, elastic networks. In this review, latest advances of cryogels containing mainly glycosaminoglycans (GAGs) or composites of GAGs and other natural or synthetic polymers are presented. Cryogels produced in this way correspond to the native extracellular matrix (ECM) in terms of both composition and molecular structure. Due to their specific structural feature and in addition to an excellent biocompatibility, GAG-based cryogels have several advantages over traditional GAG-hydrogels. This includes macroporous, interconnective pore structure, robust, elastic, and shape-memory-like mechanical behavior, as well as injectability for many GAG-based cryogels. After addressing the cryogelation process, the fabrication of GAG-based cryogels and known principles of GAG monomer crosslinking are discussed. Finally, an overview of specific GAG-based cryogels in biomedicine, mainly as polymeric scaffold material in tissue regeneration and tissue engineering-related controlled release of bioactive molecules and cells, is provided.

The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV–vis absorption spectroscopy study

Solvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore from Deinococcus radiodurans bacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an “open” (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a “closed” (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any “gating”. Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.

Linking Mechanistic Analysis of Catalytic Reactivity Cliffs to Ligand Classification

Statistical analysis of reaction data with molecular descriptors can enable chemists to identify reactivity cliffs that result from a mechanistic dependence on a specific structural feature. In this study, we develop a broadly applicable and quantitative classification workflow that identifies reactivity cliffs in eleven Ni- and Pd-catalyzed cross-coupling datasets employing monodentate phosphine ligands. A unique ligand steric descriptor, %<i>V</i>_bur (<i>min</i>), is found to divide these datasets into active and inactive regions at a similar threshold value. Organometallic studies demonstrate that this threshold corresponds to the binary outcome of bisligated versus monoligated metal and that %<i>V</i>_bur (<i>min</i>) is a physically meaningful and predictive representation of ligand structure in catalysis. Taken together, we expect that this strategy will be of broad value in mechanistic investigation of structure-reactivity relationships, while providing a means to rationally partition datasets for data-driven modeling.

Linking Mechanistic Analysis of Catalytic Reactivity Cliffs to Ligand Classification

Statistical analysis of reaction data with molecular descriptors can enable chemists to identify reactivity cliffs that result from a mechanistic dependence on a specific structural feature. In this study, we develop a broadly applicable and quantitative classification workflow that identifies reactivity cliffs in eleven Ni- and Pd-catalyzed cross-coupling datasets employing monodentate phosphine ligands. A unique ligand steric descriptor, %<i>V</i>_bur (<i>min</i>), is found to divide these datasets into active and inactive regions at a similar threshold value. Organometallic studies demonstrate that this threshold corresponds to the binary outcome of bisligated versus monoligated metal and that %<i>V</i>_bur (<i>min</i>) is a physically meaningful and predictive representation of ligand structure in catalysis. Taken together, we expect that this strategy will be of broad value in mechanistic investigation of structure-reactivity relationships, while providing a means to rationally partition datasets for data-driven modeling.

The Inhibition of Uric Acid Formation Catalyzed by Xanthine Oxidase Properties of the Alkyl Caffeates and Cardol

Xanthine oxidase inhibitors may serve as therapeutic agents for hyperuricaemia and/or oxidative stress. From our continuing investigation, we proposed that some inhibitors for reactions catalyzed by xanthine oxidase consisted of a head portion and a tail portion and that each portion had different functions for inhibition. In a previous study on the effect of alkyl gallates on the uric acid formation catalyzed by xanthine oxidase it was shown that the alkyl chain length needs to be longer than C₆ to exert inhibitory activity. In the current study, compounds having different head portions, alkyl caffeates, alkyl protocatechuates, alkyl 3,5-dihydroxybenzoates, 3,4- dihydroxyphenylalkanoates and 3,5-dihydroxyphenylalkanoates were prepared, and their effects on the uric acid formation were examined. A series of alkyl caffeates (C₁-C₁₀) was demonstrated effective in inhibiting the uric acid formation, and the inhibitory activity increased by increasing the alkyl chain length. However, none of the other compounds was effective in inhibiting the uric acid formation. These results indicate that head portions in these compounds are important for the inhibition of uric acid formation and require further a specific structural feature to elicit the inhibitory activity.

Lipoxygenase Inhibitory Activity of 6-Pentadecanylsalicylic Acid without Prooxidant Effect

6-Pentadecanylsalicylic acid, referred to as anacardic acid (C15:0), was found to inhibit the linoleic acid peroxidation competitively catalyzed by soybean lipoxygenase-1 (EC 1.13.11.12, Type 1) with an IC50 of 14.3 μM (4.88 μg/mL). This inhibition is a reversible reaction without pro-oxidant effects. The inhibition kinetics analyzed by Dixon plots indicates that anacardic acid (C15:0) is a competitive inhibitor and the inhibition constant, KI, was established as 6.4 μM. The hydrophilic head (salicylic acid) portion first chelates the iron in the active site and then the hydrophobic tail portion begins reversibly interacting with the C-terminal domain where the iron is located. The inhibition of anacardic acid (C15:0) can be explained by a combination of iron ion-chelation and hydrophobic interaction abilities because of its specific structural feature.

The ultrastructure of mink (Mustela vison) spermatozoa

The subcellular structure of epididymal spermatozoa obtained from standard dark mink was studied. Conventionally prepared thin sections were observed under a transmission electron microscope. The mink spermatozoan head showed six swellings on the dorsoventral aspects: two connected hump-like swellings at the anterior border of the equatorial segment of the acrosome, and one at the post acrosomal sheath on each side. These swellings are a species-specific structural feature which might be necessary for recognition of the ovum or attachment to it in fertilization. The neck appeared to show a dorsoventrally continuous but laterally separated capitulum which was followed by two major and five minor columns, forming at first a striated ring and then joining with the dense fibers of the axial fiber bundle. The dense fibers numbered 9, 1,5, and 6 were larger than the rest. In the axonemal complex, subfiber A was larger than the central fiber, while subfiber B was the smallest. The middle piece was of medium length when compared with other mammalian spermatozoa. The shape of the annulus was triangular in longitudinal sections. The occurrence of swellings anterior and posterior to the equatorial segment of the head and the arrangement of the connecting piece, the modified capitulum, and the grouping of the striated columns are some of the important features of mink spermatozoa.