Heterogeneous folding landscapes and predetermined breaking points within a protein family.

The accurate prediction of protein structures with artificial intelligence has been a spectacular success. Yet, how proteins fold into their native structures inside the cell remains incompletely understood. Of particular interest is to rationalize how proteins interact with the protein homeostasis network, an organism specific set of protein folding and quality control enzymes.

Kinetic Monte Carlo simulation analysis of the conductance drift in Multilevel HfO-based RRAM devices.

The drift characteristics of valence change memory (VCM) devices have been analyzed through both experimental analysis and 3D kinetic Monte Carlo (kMC) simulations. By simulating six distinct low-resistance states (LRS) over a 24-hour period at room temperature, we aim to assess the device temporal stability and retention. Our results demonstrate the feasibility of multi-level operation and reveal insights into the conductive filament (CF) dynamics.

Stimulus-Responsive Gas Marbles as an Amphibious Carrier for Gaseous Materials.

Gas marbles are a new family of particle-stabilized soft dispersed system with a soap bubble-like air-in-water-in-air structure. Herein, stimulus-responsive character is successfully introduced to a gas marble system for the first time using polymer particles carrying a poly(tertiary amine methacrylate) (pK ≈7) steric stabilizer on their surfaces as a particulate stabilizer. The gas marbles exhibited long-term stability when transferred onto the planar surface of liquid water, provided that the solution pH of the subphase is basic and neutral.

Blooming and pruning: learning from mistakes with memristive synapses.

Blooming and pruning is one of the most important developmental mechanisms of the biological brain in the first years of life, enabling it to adapt its network structure to the demands of the environment. The mechanism is thought to be fundamental for the development of cognitive skills. Inspired by this, Chialvo and Bak proposed in 1999 a learning scheme that learns from mistakes by eliminating from the initial surplus of synaptic connections those that lead to an undesirable outcome.

Single-cell expression predicts neuron-specific protein homeostasis networks.

The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing.

Calibration by differentiation - Self-supervised calibration for X-ray microscopy using a differentiable cone-beam reconstruction operator.

High-resolution X-ray microscopy (XRM) is gaining interest for biological investigations of extremely small-scale structures. XRM imaging of bones in living mice could provide new insights into the emergence and treatment of osteoporosis by observing osteocyte lacunae, which are holes in the bone of few micrometres in size. Imaging living animals at that resolution, however, is extremely challenging and requires very sophisticated data processing converting the raw XRM detector output into reconstructed images.

Ultralow-parameter denoising: Trainable bilateral filter layers in computed tomography.

Background: Computed tomography (CT) is widely used as an imaging tool to visualize three-dimensional structures with expressive bone-soft tissue contrast. However, CT resolution can be severely degraded through low-dose acquisitions, highlighting the importance of effective denoising algorithms.

Purpose: Most data-driven denoising techniques are based on deep neural networks, and therefore, contain hundreds of thousands of trainable parameters, making them incomprehensible and prone to prediction failures.

Functional network motifs defined through integration of protein-protein and genetic interactions.

Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks.

A Low-Power RRAM Memory Block for Embedded, Multi-Level Weight and Bias Storage in Artificial Neural Networks.

Pattern recognition as a computing task is very well suited for machine learning algorithms utilizing artificial neural networks (ANNs). Computing systems using ANNs usually require some sort of data storage to store the weights and bias values for the processing elements of the individual neurons. This paper introduces a memory block using resistive memory cells (RRAM) to realize this weight and bias storage in an embedded and distributed way while also offering programming and multi-level ability.

Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling.

Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo-seq) has revolutionized the study of translation by revealing many of its underlying mechanisms.

Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2.

RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis.

Programmed Trade-offs in Protein Folding Networks.

Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb.

Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation.

Background: Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete.

Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis.

Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation and degradation.

Coping with stress by regulating tRNAs.

Stress conditions curtail the energetically costly process of messenger RNA translation. In this issue of , Torrent report key evidence for a direct link between codon usage and translation regulation in response to stress.

Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation.

Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution.

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo.

The genetic code allows most amino acids a choice of optimal and nonoptimal codons. We report that synonymous codon choice is tuned to promote interaction of nascent polypeptides with the signal recognition particle (SRP), which assists in protein translocation across membranes. Cotranslational recognition by the SRP in vivo is enhanced when mRNAs contain nonoptimal codon clusters 35-40 codons downstream of the SRP-binding site, the distance that spans the ribosomal polypeptide exit tunnel.

Interplay between chaperones and protein disorder promotes the evolution of protein networks.

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability.

Principles of cotranslational ubiquitination and quality control at the ribosome.

Achieving efficient cotranslational folding of complex proteomes poses a challenge for eukaryotic cells. Nascent polypeptides that emerge vectorially from the ribosome often cannot fold stably and may be susceptible to misfolding and degradation. The extent to which nascent chains are subject to cotranslational quality control and degradation remains unclear.

The ribosome as a hub for protein quality control.

Cells face a constant challenge as they produce new proteins. The newly synthesized polypeptides must be folded properly to avoid aggregation. If proteins do misfold, they must be cleared to maintain a functional and healthy proteome.

The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis.

In eukaryotic cells a molecular chaperone network associates with translating ribosomes, assisting the maturation of emerging nascent polypeptides. Hsp70 is perhaps the major eukaryotic ribosome-associated chaperone and the first reported to bind cotranslationally to nascent chains. However, little is known about the underlying principles and function of this interaction.

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.

The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear. Here, we derive a revised translational efficiency scale that incorporates the competition between tRNA supply and demand.

The molecular architecture of the eukaryotic chaperonin TRiC/CCT.

TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. Previously proposed TRiC models differ substantially in their subunit arrangements and ring register.

Identification of novel functional inhibitors of acid sphingomyelinase.

We describe a hitherto unknown feature for 27 small drug-like molecules, namely functional inhibition of acid sphingomyelinase (ASM). These entities named FIASMAs (Functional Inhibitors of Acid SphingoMyelinAse), therefore, can be potentially used to treat diseases associated with enhanced activity of ASM, such as Alzheimer's disease, major depression, radiation- and chemotherapy-induced apoptosis and endotoxic shock syndrome. Residual activity of ASM measured in the presence of 10 µM drug concentration shows a bimodal distribution; thus the tested drugs can be classified into two groups with lower and higher inhibitory activity.

Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.

Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell. Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization. Despite the extensive efforts, little is known about the specificity of the chaperones and other factors that bind nascent polypeptides.