Opening Amyloid-Windows to the secondary structure of proteins: The amyloidogenecity increases tenfold inside beta-sheets.

Methods from artificial intelligence (AI), in general, and machine learning, in particular, have kept conquering new territories in numerous areas of science. Most of the applications of these techniques are restricted to the classification of large data sets, but new scientific knowledge can seldom be inferred from these tools. Here we show that an AI-based amyloidogenecity predictor can strongly differentiate the border- and the internal hexamers of ß-pleated sheets when screening all the Protein Data Bank-deposited homology-filtered protein structures. Our main result shows that more than 30% of internal hexamers of ß sheets are predicted to be amyloidogenic, while just outside the border regions, only 3% are predicted as such. This result may elucidate a general protection mechanism of proteins against turning into amyloids: if the borders of ß-sheets were amyloidogenic, then the whole ß sheet could turn more easily into an insoluble amyloid-structure, characterized by periodically repeated parallel ß-sheets. We also present that no analogous phenomenon exists on the borders of α-helices or randomly chosen subsequences of the studied protein structures.

Sensor-Enhanced Smart Gripper Development for Automated Meat Processing.

Grasping and object manipulation have been considered key domains of Cyber-Physical Systems (CPS) since the beginning of automation, as they are the most common interactions between systems, or a system and its environment. As the demand for automation is spreading to increasingly complex fields of industry, smart tools with sensors and internal decision-making become necessities. CPS, such as robots and smart autonomous machinery, have been introduced in the meat industry in recent decades; however, the natural diversity of animals, potential anatomical disorders and soft, slippery animal tissues require the use of a wide range of sensors, software and intelligent tools. This paper presents the development of a smart robotic gripper for deployment in the meat industry. A comprehensive review of the available robotic grippers employed in the sector is presented along with the relevant recent research projects. Based on the identified needs, a new mechatronic design and early development process of the smart gripper is described. The integrated force sensing method based on strain measurement and magnetic encoders is described, including the adjacent laboratory and on-site tests. Furthermore, a combined slip detection system is presented, which relies on an optical flow-based image processing algorithm using the video feed of a built-in endoscopic camera. Basic user tests and application assessments are presented.

Assessment of Surgeons' Stress Levels with Digital Sensors during Robot-Assisted Surgery: An Experimental Study.

Robot-Assisted Minimally Invasive Surgery (RAMIS) marks a paradigm shift in surgical procedures, enhancing precision and ergonomics. Concurrently it introduces complex stress dynamics and ergonomic challenges regarding the human-robot interface and interaction. This study explores the stress-related aspects of RAMIS, using the da Vinci XI Surgical System and the Sea Spikes model as a standard skill training phantom to establish a link between technological advancement and human factors in RAMIS environments. By employing different physiological and kinematic sensors for heart rate variability, hand movement tracking, and posture analysis, this research aims to develop a framework for quantifying the stress and ergonomic loads applied to surgeons. Preliminary findings reveal significant correlations between stress levels and several of the skill-related metrics measured by external sensors or the SURG-TLX questionnaire. Furthermore, early analysis of this preliminary dataset suggests the potential benefits of applying machine learning for surgeon skill classification and stress analysis. This paper presents the initial findings, identified correlations, and the lessons learned from the clinical setup, aiming to lay down the cornerstones for wider studies in the fields of clinical situation awareness and attention computing.

Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments.

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.

Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining.

Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.

A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins.

How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. Forty-eight percent of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families whose transcripts are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs, which are introduced for the first time here. All four families have sequence properties that drive phase separation and we demonstrate phase separation for one exemplar in vitro. This systematic analysis represents the first blueprint for cuticle construction and highlights the massive contribution that phase-separating materials make to the structure.

The multiple alignments of very short sequences.

The multiple sequence alignment (MSA) is an increasingly important task in bioinformatics as we have to deal with the constantly increasing gene- and protein sequence databases. MSA is applied in phylogenetic analysis, in discovering conservative protein domains, in the assignment of secondary and tertiary structural features in proteins, or in the metagenomic sample analysis and gene discovery. Usually, the focus is on the MSA of long sequences, since in the practice these tasks appear most frequently. However, the strict analysis of the optimal MSA of short sequences is an area of negligence, and findings there may contribute to better and faster algorithms for the multiple alignment of long sequences. In the present contribution, we are examining length-1 sequences using arbitrary metric and length-2 sequences using unit metric, and we show that the optimum of the MSA problem can be achieved by the trivial alignment in both cases.

On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection.

The Protein Data Bank (PDB) today contains more than 174,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting properties for different applications. Our research group prepared an automatically updated list of amyloid- and probably amyloidogenic molecules, the PDB_Amyloid collection, which is freely available at the address http://pitgroup.org/amyloid. This resource applies exclusively the geometric properties of the steric structures for identifying amyloids. In the present contribution, we analyze the starting (i.e., prefix) subsequences of the characteristic, parallel beta-sheets of the structures in the PDB_Amyloid collection, and identify further appearances of these length-5 prefix subsequences in the whole PDB data set. We have identified this way numerous proteins, whose normal or irregular functions involve amyloid formation, structural misfolding, or anti-coagulant properties, simply by containing these prefixes: including the T-cell receptor (TCR), bound with the major histocompatibility complexes MHC-1 and MHC-2; the p53 tumor suppressor protein; a mycobacterial RNA polymerase transcription initialization complex; the human bridging integrator protein BIN-1; and the tick anti-coagulant peptide TAP.

PDB_Amyloid: an extended live amyloid structure list from the PDB.

The Protein Data Bank (PDB) contains more than 135 000 entries at present. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, most amyloid structures deposited in the PDB are in the form of solid state NMR data. Based on the geometric analysis of these deposited structures, we have prepared an automatically updated web server, which generates a list of the deposited amyloid structures, and also entries of globular proteins that have amyloid-like substructures of given size and characteristics. We have found that by applying only appropriately selected geometric conditions, it is possible to identify deposited amyloid structures and a number of globular proteins with amyloid-like substructures. We have analyzed these globular proteins and have found proof in the literature that many of them form amyloids more easily than many other globular proteins. Our results relate to the method of Stankovic et al. [Stankovic I et al. (2017) IPSI BgD Tran Int Res 13, 47-51], who applied a hybrid textual-search and geometric approach for finding amyloids in the PDB. If one intends to identify a subset of the PDB for certain applications, the identification algorithm needs to be re-run periodically, since in 2017 on average 30 new entries per day were deposited in the data bank. Our web server is updated regularly and automatically, and the identified amyloid and partial amyloid structures can be viewed or their list can be downloaded from the following website https://pitgroup.org/amyloid.