Rhomboid-catalyzed intramembrane proteolysis requires hydrophobic matching with the surrounding lipid bilayer

Membrane thinning by rhomboid proteins has been proposed to reduce hydrophobic mismatch, providing a unique environment for important functions ranging from intramembrane proteolysis to retrotranslocation in protein degradation. We show by in vitro reconstitution and solid-state nuclear magnetic resonance that the lipid environment of the Escherichia coli rhomboid protease GlpG influences its activity with an optimal hydrophobic membrane thickness between 24 and 26 Å. While phosphatidylcholine membranes are only negligibly altered by GlpG, in an E. coli-relevant lipid mix of phosphatidylethanolamine and phosphatidylglycerol, a thinning by 1.1 Å per leaflet is observed. Protease activity is strongly correlated with membrane thickness and shows no lipid headgroup specificity. We infer from these results that, by adjusting the thickness of specific membrane domains, membrane proteins shape the bilayer for their specific needs.

ProteinPrompt: a webserver for predicting protein-protein interactions

Motivation

Protein-protein interactions (PPIs) play an essential role in a great variety of cellular processes and are therefore of significant interest for the design of new therapeutic compounds as well as the identification of side effects due to unexpected binding. Here, we present ProteinPrompt, a webserver that uses machine learning algorithms to calculate specific, currently unknown PPIs. Our tool is designed to quickly and reliably predict contact propensities based on an input sequence in order to scan large sequence libraries for potential binding partners, with the goal to accelerate and assure the quality of the laborious process of drug target identification.

Results

We collected and thoroughly filtered a comprehensive database of known binders from several sources, which is available as download. ProteinPrompt provides two complementary search methods of similar accuracy for comparison and consensus building. The default method is a random forest (RF) algorithm that uses the auto-correlations of seven amino acid scales. Alternatively, a graph neural network (GNN) implementation can be selected. Additionally, a consensus prediction is available. For each query sequence, potential binding partners are identified from a protein sequence database. The proteom of several organisms are available and can be searched for binders. To evaluate the predictive power of the algorithms, we prepared a test dataset that was rigorously filtered for redundancy. No sequence pairs similar to the ones used for training were included in this dataset. With this challenging dataset, the RF method achieved an accuracy rate of 0.88 and an area under the curve of 0.95. The GNN achieved an accuracy rate of 0.86 using the same dataset. Since the underlying learning approaches are unrelated, comparing the results of RF and GNNs reduces the likelihood of errors. The consensus reached an accuracy of 0.89.

Availability and implementation

ProteinPrompt is available online at: http://proteinformatics.org/ProteinPrompt, where training and test data used to optimize the methods are also available. The server makes it possible to scan the human proteome for potential binding partners of an input sequence within minutes. For local offline usage, we furthermore created a ProteinPrompt Docker image which allows for batch submission: https://gitlab.hzdr.de/proteinprompt/ProteinPrompt. In conclusion, we offer a fast, accurate, easy-to-use online service for predicting binding partners from an input sequence.

Structural Studies on the Inhibitory Binding Mode of Aromatic Coumarinic Esters to Human Kallikrein-Related Peptidase 7

The serine protease kallikrein-related peptidase 7 (KLK7) is a member of the human tissue kallikreins. Its dysregulation leads to pathophysiological inflammatory processes in the skin. Furthermore, it plays a role in several types of cancer. For the treatment of KLK7-associated diseases, coumarinic esters have been developed as small-molecule enzyme inhibitors. To characterize the inhibition mode of these inhibitors, we analyzed structures of the inhibited protease by X-ray crystallography. Electron density shows the inhibitors covalently attached to His57 of the catalytic triad. This confirms the irreversible character of the inhibition process. Upon inhibitor binding, His57 undergoes an outward rotation; thus, the catalytic triad of the protease is disrupted. Besides, the halophenyl moiety of the inhibitor was absent in the final enzyme-inhibitor complex due to the hydrolysis of the ester linkage. With these results, we analyze the structural basis of KLK7 inhibition by the covalent attachment of aromatic coumarinic esters.

Kallikrein-related peptidase 14 is the second KLK protease targeted by the serpin vaspin

Kallikrein-related peptidases KLK5, KLK7 and KLK14 are important proteases in skin desquamation and aberrant KLK activity is associated with inflammatory skin diseases such as Netherton syndrome but also with various serious forms of cancer. Previously, we have identified KLK7 as the first protease target of vaspin (Serpin A12). Here, we report KLK14 as a second KLK protease to be inhibited by vaspin. In conclusion, vaspin represents a multi-specific serpin targeting the kallikrein proteases KLK7 and KLK14, with distinct exosites regulating recognition of these target proteases and opposing effects of heparin binding on the inhibition reaction.

Glycosylation of human vaspin (SERPINA12) and its impact on serpin activity, heparin binding and thermal stability

Vaspin is a glycoprotein with three predicted glycosylation sites at asparagine residues located in proximity to the reactive center loop and close to domains that play important roles in conformational changes underlying serpin function. In this study, we have investigated the glycosylation of human vaspin and its effects on biochemical properties relevant to vaspin function. We show that vaspin is modified at all three sites and biochemical data demonstrate that glycosylation does not hinder inhibition of the target protease kallikrein 7. Although binding affinity to heparin is slightly decreased, the protease inhibition reaction is still significantly accelerated in the presence of heparin. Glycosylation did not affect thermal stability.

Basic Residues of β-Sheet A Contribute to Heparin Binding and Activation of Vaspin (Serpin A12)

Many members of the serine protease inhibitor (serpin) family are activated by glycosaminoglycans (GAGs). Visceral adipose tissue-derived serpin (vaspin), serpin A12 of the serpin family, and its target protease kallikrein 7 (KLK7) are heparin-binding proteins, and inhibition of KLK7 by vaspin is accelerated by heparin. However, the nature of GAG binding to vaspin is not known. Here, we measured vaspin binding of various glycosaminoglycans and low molecular weight heparins by microscale thermophoresis and analyzed acceleration of protease inhibition by these molecules. In addition, basic residues contributing to heparin binding and heparin activation were identified by a selective labeling approach. Together, these data show that vaspin binds heparin with high affinity (K_D = 21 ± 2 nm) and that binding takes place at a basic patch on top of β-sheet A and is different from other heparin-binding serpins. Mutation of basic residues decreased heparin binding and activation of vaspin. Similarly, reactive center loop insertion into sheet A decreased heparin binding because it disturbs the basic cluster. Finally, using vaspin-overexpressing keratinocyte cells, we show that a significant part of secreted vaspin is bound in the extracellular matrix on the cell surface. Together, basic residues of central β-sheet A contribute to heparin binding and activation of vaspin. Thus, binding to GAGs in the extracellular matrix can direct and regulate vaspin interaction with target proteases or other proteins and may play an important role in the various beneficial functions of vaspin in different tissues.

Crystal structure of cleaved vaspin (serpinA12)

The adipokine vaspin (serpinA12) is mainly expressed in white adipose tissue and exhibits various beneficial effects on obesity-related processes. Kallikrein 7 is the only known target protease of vaspin and is inhibited by the classical serpin inhibitory mechanism involving a cleavage of the reactive center loop between P1 (M378) and P1' (E379). Here, we present the X-ray structure of vaspin, cleaved between M378 and E379. We provide a comprehensive analysis of differences between the uncleaved and cleaved forms in the shutter, breach, and hinge regions with relation to common molecular features underlying the serpin inhibitory mode. Furthermore, we point out differences towards other serpins and provide novel data underlining the remarkable stability of vaspin. We speculate that the previously reported FKGx1Wx2x3 motif in the breach region may play a decisive role in determining the reactive center loop configuration in the native vaspin state and might contribute to the high thermostability of vaspin. Thus, this structure may provide a basis for future mutational studies.

Three-dimensional organic microlasers with low lasing thresholds fabricated by multiphoton and UV lithography

Cuboid-shaped organic microcavities containing a pyrromethene laser dye and supported upon a photonic crystal have been investigated as an approach to reducing the lasing threshold of the cavities. Multiphoton lithography facilitated fabrication of the cuboid cavities directly on the substrate or on the decoupling structure, while similar structures were fabricated on the substrate by UV lithography for comparison. Significant reduction of the lasing threshold by a factor of ~30 has been observed for cavities supported by the photonic crystal relative to those fabricated on the substrate. The lasing mode spectra of the cuboid microresonators provide strong evidence showing that the lasing modes are localized in the horizontal plane, with the shape of an inscribed diamond.

Cervical artery dissection: An atypical presentation with Ehlers-Danlos-like collagen pathology?

The authors took skin biopsies of the macroscopically normal skin of seven consecutive patients with spontaneous cervical artery dissection (SCAD). Histologically, alterations of the collagen and elastic fiber networks were found in six patients. In five, the histologic, immunohistochemical, and ultrastructural changes were similar to those usually found in Ehlers-Danlos syndrome (EDS). This suggests that SCAD is frequently associated with the dermal alterations seen in EDS.

[Benign disorders of soft tissue on the roentgen computer tomogram]

Diagnostic procedures of soft tissue lesions have considerably improved by the high density resolution of computed tomography. Indications for investigations by CT are described in detail and illustrated by examples. Enhancement by contrast medium enables further differentiation of the tumors. In most cases for cancer control the scar tissue can be differentiated from relapse. Comparison of both sides reveals isodense tumors. Limits of the CT method will be met in looking for discreet changes in the joints.

[Problems of differentiating sacral fractures and fissure formations in the sacrum]

It is shown on the basis of two observations that computed tomography represents a valuable additional means to clarify the diagnosis of congenital and traumatic changes in the pelvis, especially the sacrum and vertebral column. The article explains the differential diagnosis between congenital fissures of the pelvic arch and fractures by means of computed tomography. This is illustrated with the help of x-ray morphologic criteria.

[Problems in radiology of concealed lung disorders (author's transl)]

The problems of diagnostic radiology in dealing with discreet and difficult to find pathological lung conditions are demonstrated by typical examples. Special emphasis is given to localized changes found in paramediastinal and paracardial regions of the lung and the diaphragm. Special attention was given to patients with elusive or hidden lung disorders and the value of information by X-rays of more than one dimension, by spot films taken during fluoroscopy, by bronchography, by tomography, and by computed tomography is discussed. Early diagnosis of lung and bronchial carcinoma as well as infections of the lung parenchyma can only be found, if the radiological methods are optimally used.