Mechanisms and pathology of protein misfolding and aggregation

Thermodynamics for reduced models of polymer aggregation based on maximum entropy principle

Polymeric aggregates play a significant role in biology and chemical engineering. In order to make a clear description of their underlying formation procedure, simplified models are crucial because the original mass-action equations involve numerous variables, complicating analysis and understanding. While the dynamical aspects of simplified models have been widely studied, their thermodynamic properties are less understood. In this study, we explore the Maximum Entropy Principle (MEP)-reduced models, initially developed for dynamical analysis, from a brand-new thermodynamic perspective. Analytical expressions, along with numerical simulations, demonstrate that the discrete MEP-reduced model strictly retains laws of thermodynamics, which holds true even when the aggregate size transits from discrete values to continuous real numbers. Our findings not only clarify the thermodynamic consistency between the MEP-reduced models and the original models of polymeric aggregates for the first time but also suggest avenues for future research into the model-reduction thermodynamics.

Acid-Resistant and Viscosity-Sensitive Proteome Aggregation Sensor To Visualize Cellular Aggrephagy in Live Cells and Clinical Samples

Aggrephagy in cells is defined as the degradation of intracellular aggregated proteins via the macroautophagy process. This process sequesters protein aggregates into autolysosomes, which bear characteristic viscous and acidic microenvironments. Limited protein aggregation sensors are environmentally compatible with the cellular aggrephagy process. Here, we report an acid-resistant and viscosity-sensitive proteome aggregation sensor to detect cellular aggrephagy in stressed cells and clinical samples. This sensor fluoresces upon selectively and ubiquitously binding to different aggregated proteins. Importantly, unlike other reported protein aggregation sensors, our probe offers unique acid-resistant fluorescence inside aggregated proteins, enabling its application in the acidic autolysosome microenvironment. In live cells under various stressed conditions, the optimal probe (A6) successfully detects aggregated proteome in autolysosomes, as validated by colocalization with a lysosomal tracker. Additionally, we demonstrate that the sensor can detect proteome aggregation in heat-stressed clinical tissue samples biopsied from cancer patients undergoing thermal perfusion treatment. Together, the reported acid-resistant and viscosity-sensitive protein aggregation sensor facilitates the detection of cellular aggrephagy by chemically matching its microenvironmental characteristics.

Strategic Modulation of Polarity and Viscosity Sensitivity of Bimane Molecular Rotor-Based Fluorophores for Imaging α-Synuclein

Molecular rotor-based fluorophores (RBFs) that are target-selective and sensitive to both polarity and viscosity are valuable for diverse biological applications. Here, we have designed next-generation RBFs based on the underexplored bimane fluorophore either through a change in aryl substitution or varying π-linkages between the rotatable electron donors and acceptors to produce red-shifted fluorescence emissions with large Stokes shifts. RBFs exhibit a twisted intramolecular charge transfer mechanism that enables control of polarity and viscosity sensitivity as well as target selectivity. These features enable their application in (1) turn-on fluorescent detection of α-synuclein (αS) fibrils, a hallmark of Parkinson's disease, including amplified fibrils from patient samples; (2) monitoring early misfolding and oligomer formation during αS aggregation; and (3) selective imaging of αS condensates formed by liquid-liquid phase separation. In all three cases, we show that our probes have high levels of selectivity for αS compared to other aggregating proteins. These properties enable one to study the interplay of αS and tau in amyloid aggregation and the mechanisms underlying neurodegenerative disorders.

Leveraging heterocycle-fused 1,4-benzoquinone to design chemical modulators for both metal-free and metal-bound amyloid-β

The complex pathology of Alzheimer's disease includes various pathogenic components, such as metal-free amyloid-β (Aβ) and metal-bound Aβ (metal-Aβ). Here we report an effective strategy for developing novel heterocycle-fused 1,4-benzoquinone (BQ) compounds to control the aggregation and toxicity of both metal-free Aβ and metal-Aβ. We designed and synthesized these compounds by fusing BQ with 3-pyrazolone responsible for metal chelation. The compounds' ability to form covalent bonds with Aβ is tuned by the annulation of the BQ moiety and the type, position, and number of substituents on the 3-pyrazolone group. Furthermore, the BQ functionality on the 3-pyrazolone framework can undergo o-hydroxylation, enhancing its metal chelation in a bidentate manner. Our results demonstrate that these heterocycle-fused BQ compounds can redirect the assembly of Aβ into less toxic aggregates by binding to metal ions, modifying Aβ structures in both the absence and presence of metal ions, and promoting oxidative changes to Aβ. This study highlights the importance of structural modifications and optimizations of BQ to leverage its strength of covalently cross-linking to Aβ and overcome its limitations in metal chelation and cytotoxicity, which are critical for designing chemical modulators for metal-free Aβ and metal-Aβ. Our approach offers a novel strategy for developing chemical modulators towards metal-related peptides and proteins as well as therapeutic agents for metal-associated amyloid disorders.

The outcast of medicine: metals in medicine--from traditional mineral medicine to metallodrugs

Metals have long held a significant role in the human body and have been utilized as mineral medicines for thousands of years. The modern advancement of metals in pharmacology, particularly as metallodrugs, has become crucial in disease treatment. As the machanism of metallodurgsare increasingly uncovered, some metallodrugs are already approved by FDA and widely used in treating antitumor, antidiabetes, and antibacterial. Therefore, a thorough understanding of metallodrug development is essential for advancing future study. This review offers an in-depth examination of the evolution of mineral medicines and the applications of metallodrugs within contemporary medicine. We specifically aim to summarize the historical trajectory of metals and mineral medicines in Traditional Chinese Mineral Medicine by analyzing key historical texts and representative mineral medicines. Additionally, we discuss recent advancements in understanding metallodrugs' mechanisms, such as protein interactions, enzyme inhibition, DNA interactions, reactive oxygen species (ROS) generation, and cellular structure targeting. Furthermore, we address the challenges in metallodrug development and propose potential solutions. Lastly, we outline future directions for metallodrugs to enhance their efficacy and effectiveness. The progression of metallodrugs has broadened their applications and contributed significantly to patient health, creating good healthcare solutions for the global population.

Ultrasensitive Differential Scanning Calorimetric (US-DSC) Study of the Thermal-Induced Dynamic Transition Behaviors of PEO-PPO-PEO in Aqueous Solution

Temperature-responsive macromolecules can provide insights into the mechanisms of the aggregation and precipitation processes of proteins. In this study, the PEO-PPO-PEO triblock copolymer, Pluronic P123, has been utilized as a protein model to investigate the thermally induced dynamic transition behavior by ultrasensitive differential scanning calorimetry (US-DSC). The results of US-DSC reveal hysteresis in the disaggregation process of P123 micelles. Combined with the particle size distribution, a stepwise disaggregation mechanism is proposed. The disaggregation of P123 micelles in the cooling process involved rod-to-sphere transition, fragmentation, and dissolution of micelles. Moreover, US-DSC results show that both the sphere-to-rod transition and micelle fragmentation are dependent on the scanning rate and reveal the relationship between the dynamic transition and thermodynamic properties of P123. These findings expand the understanding not only of aggregation and disaggregation of P123 in dilute aqueous systems but also of the thermal unfolding and aggregation of proteins.

Unraveling the catalase dynamics: Biophysical and computational insights into co-solutes driven stabilization under extreme pH conditions

Catalase plays a vital role in eliminating toxic peroxides from the human body and the environment. The versatile applications of this enzyme extend across biotechnological industries and innovative bioremediation approaches. Nonetheless, ensuring enzyme stability is a challenging task. This study investigated the efficacy of co-solutes (glucose and dextran 70) as stabilizing agents for catalase under denaturing pH conditions by employing a combination of spectroscopic techniques (UV-visible, circular dichroism, and Trp fluorescence), calorimetric measurements (DSC and ITC), enzymatic assay, and in silico studies. The results of spectroscopic and thermal stability studies indicated that the co-solutes tend to stabilize catalase, even under extreme pH conditions. Molecular docking and ITC findings showed that glucose has a higher binding tendency to catalase than dextran 70. MD simulations further underscore reduced structural deviations (RMSF and RMSD), compact structure (Rg and SASA), and formation of H-bonds between catalase and co-solutes, complementing the in vitro observations. This study contributes to the understanding of enzyme stability under suboptimal pH conditions and paves the way for the development of more robust enzyme formulations suitable for a range of applications.

The Regulation of TDP-43 Structure and Phase Transitions: A Review

The transactive response DNA binding protein 43 (TDP-43) is an RNA/DNA-binding protein that is involved in a number of cellular functions, including RNA processing and alternative splicing, RNA transport and translation, and stress granule assembly. It has attracted significant attention for being the primary component of cytoplasmic inclusions in patients with amyotrophic lateral sclerosis or frontotemporal dementia. Mounting evidence suggests that both cytoplasmic aggregation of TDP-43 and loss of nuclear TDP-43 function contribute to TDP-43 pathology. Furthermore, recent studies have demonstrated that TDP-43 is an important component of many constitutive or stress-induced biomolecular condensates. Dysregulation or liquid-to-gel transition of TDP-43 condensates can lead to alterations in TDP-43 function and the formation of TDP-43 amyloid fibrils. In this review, we summarize recent research progress on the structural characterization of TDP-43 and the TDP-43 phase transition. In particular, the roles that disease-associated genetic mutations, post-translational modifications, and extrinsic stressors play in the transitions among TDP-43 monomers, liquid condensates, solid condensates, and fibrils are discussed. Finally, we discuss the effectiveness of available regulators of TDP-43 phase separation and aggregation. Understanding the underlying mechanisms that drive the pathological transformation of TDP-43 could help develop therapeutic strategies for TDP-43 pathology.

Dependence of mitochondrial calcium signalling and dynamics on the disaggregase, CLPB

Cells utilize protein disaggregases to avoid abnormal protein aggregation that causes many diseases. Among these, caseinolytic peptidase B protein homolog (CLPB) is localized in the mitochondrial intermembrane space and linked to human disease. Upon CLPB loss, MICU1 and MICU2, regulators of the mitochondrial calcium uniporter complex (mtCU), and OPA1, a main mediator of mitochondrial fusion, become insoluble but the functional outcome remains unclear. In this work we demonstrate that CLPB is required to maintain mitochondrial calcium signalling and fusion dynamics. CLPB loss results in altered mtCU composition, interfering with mitochondrial calcium uptake independently of cytosolic calcium and mitochondrial membrane potential. Additionally, OPA1 decreases, and aggregation occurs, accompanied by mitochondrial fragmentation. Disease-associated mutations in the CLPB gene present in skin fibroblasts from patients also display mitochondrial calcium and structural changes. Thus, mtCU and fusion activity are dependent on CLPB, and their impairments might contribute to the disease caused by CLPB variants.

High-Resolution Mass Spectrometry Approach for Proteomic and Metabolomic Analyses of High-Protein Soybean Seeds

Soybeans are a valuable source of vegetable protein and edible oil. Fast neutron (FN) radiation was employed to produce large chromosomal deletions in soybean Glycine max (L.) Merrill. We conducted proteomic and metabolomic profiling of a high-protein soybean mutant (G15FN-12) developed through FN mutagenesis to identify the metabolic pathways that underlie the elevated protein content. A deletion of 137 genes located on chromosome-12 had occurred in G15FN-12. Tandem tag-based protein profiling of the mutant and wild type identified 6098 proteins, of which 175 showed increased abundance and 239 showed decreased abundance in the mutant seeds. Using liquid chromatography-mass spectrometry (LC-MS)-based metabolomic profiling, we identified 610 metabolites, of which 294 metabolites showed increased and 157 showed reduced content in mutant seeds as compared to wild type. Proteomic and metabolomic profiling revealed a decrease in ubiquitin-proteasome-associated proteins and an increase in heat shock proteins in the mutant seed. We hypothesize that decreased protein degradation, together with enhanced refolding of misfolded protein by molecular chaperones, contributes to elevated protein content in the mutant seed. The development of value-added seed traits such as increased protein using advanced metabolic engineering techniques can be achieved by further exploring the metabolic pathways identified in this investigation.

Interaction of native and aggregated albumin with DMPC bilayers

The study of protein-lipid interaction offers interesting insights into the mutual alterations determined in the formation of the supramolecular complex. It gains even more interest, not only in basic research but also in biomedical and biomaterial applications, when protein aggregation and fibril formation are involved. In this study, the reciprocal influence of human serum albumin (HSA), in both the native and the thermally aggregated state, and dimyristoylphosphatidylcholine (DMPC) bilayers is investigated by combining UV-Vis scattering, attenuated total reflection Fourier transform infrared (ATR-FTIR), and spin-label electron paramagnetic resonance (EPR) spectroscopies. Temperature-dependent optical density at fixed wavelength reveals the pre- and the main phase transitions in DMPC bilayers as well as the onset of protein aggregation at Tagg ≈ 70 °C. In native protein/lipid complexes, the protein adsorption on the membrane surfaces suppresses the pre-transition and downshifts the temperature of the main phase transitions of DMPC, whereas the presence of DMPC increases Tagg without affecting the thermal profile. Kinetics experiments reveal that lipid bilayers reduce the thermally-induced aggregation of the protein. ATR-FTIR data indicate that albumin weakens the hydrogen bonding network at the carbonyl groups of the membrane. Conversely, lipid bilayers in any physical state do not alter the structural features of both native and aggregated HSA. In protein/lipid complexes, spin-label EPR of the lipid component reveals that the proteins reduce the packing density of the first chain segments and stabilize the fluid state, the effect being more evident for the native protein.

Advances in the structures, mechanisms and targeting of molecular chaperones

Molecular chaperones, a class of complex client regulatory systems, play significant roles in the prevention of protein misfolding and abnormal aggregation, the modulation of protein homeostasis, and the protection of cells from damage under constantly changing environmental conditions. As the understanding of the biological mechanisms of molecular chaperones has increased, their link with the occurrence and progression of disease has suggested that these proteins are promising targets for therapeutic intervention, drawing intensive interest. Here, we review recent advances in determining the structures of molecular chaperones and heat shock protein 90 (HSP90) chaperone system complexes. We also describe the features of molecular chaperones and shed light on the complicated regulatory mechanism that operates through interactions with various co-chaperones in molecular chaperone cycles. In addition, how molecular chaperones affect diseases by regulating pathogenic proteins has been thoroughly analyzed. Furthermore, we focus on molecular chaperones to systematically discuss recent clinical advances and various drug design strategies in the preclinical stage. Recent studies have identified a variety of novel regulatory strategies targeting molecular chaperone systems with compounds that act through different mechanisms from those of traditional inhibitors. Therefore, as more novel design strategies are developed, targeting molecular chaperones will significantly contribute to the discovery of new potential drugs.

Fluorescent Fingerprint Identification of Protein Structural Changes and Disease-Specific Amyloid Beta Aggregates Based on a Single-Nanozyme Sensor Array

The misfolding of amyloid β (Aβ) peptides into an aggregation state is a central hallmark of the onset of Alzheimer's disease (AD). However, conventional methods are mainly focused on detecting a specific Aβ peptide, which makes it difficult to recognize multiple analytes with different topological features and unfolded states at the same time. Here, we propose a simple and universal sensing strategy to construct a fluorescence sensor array by using a single-nanozyme probe combined with three fluorescent substrates as three recognition units to probe the protein structural changes and identify between multiple Aβ assemblies. In this sensor system, the fingerprint-like patterns are produced from the nonspecific interactions between topological proteins and the sensing units. As a result, this sensor array can accurately identify 13 kinds of proteins and their mixtures at different ratios. Moreover, the sensor array can discriminate against proteins with unfolded states and diverse conformational forms. Most importantly, the sensor array successfully distinguishes between multiple Aβ species, even in artificial cerebrospinal fluid samples and human serum samples. This work provides an attractive and reliable strategy for predicting pathologically relevant proteins and clinical diagnosis of AD.

No structure, no problem: Protein stabilization by Hero proteins and other chaperone-like IDPs

In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date, and based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.

Pathogenic variants in the fibronectin type III domain of leptin receptor: Molecular dynamics simulation and structural analysis

Several case reports have identified leptin receptor (LEPR) variants associated with severe obesity in humans. However, the structure of LEPR has only been partially understood until recently, and few studies have investigated the detrimental effects of these variants on the protein's three-dimensional structure. Notably, fibronectin type III (FnIII) domains play a crucial role in signal transduction. In this study, we examined the impact of 10 variants within the FnIII domains on LEPR structure using molecular dynamics (MD) simulations and structural analysis. Our 300 ns MD simulations revealed that the C604S variant, which disrupts a key disulfide bond, significantly increased the overall root-mean-square deviation (RMSD) of the FnIII-2 and FnIII-3 domains, indicating destabilization of the interdomain rigidity required for proper signaling. Variants such as P639L, N718S, and W646C also induced abnormal bending and rotational misalignment between the FnIII domains, contributing to interdomain destabilization. Structural analysis identified folding nuclei and demonstrated that L662S, W664R, H684P, and S723F destabilize the internal domain. Variants affecting interdomain resulted in lower-than-expected damage prediction scores by bioinformatics tools. This study is expected to contribute to the elucidation of the disease-causing mechanisms of missense variants in the leptin receptor.

Rational design of peptides to overcome drug resistance by metabolic regulation

Chemotherapy is widely used clinically, however, its efficacy is often compromised by the development of drug resistance, which arises from prolonged administration of drugs or other stimuli. One of the driven causes of drug resistance in tumors or bacterial infections is metabolic reprogramming, which alters mitochondrial metabolism, disrupts metabolic pathways and causes ion imbalance. Bioactive peptide materials, due to their biocompatibility, diverse bioactivities, customizable sequences, and ease of modification, have shown promise in overcoming drug resistance. This review provides an in-depth analysis of metabolic reprogramming and associated microenvironmental changes that contribute to drug resistance in common tumors and bacterial infections, suggesting potential therapeutic targets. Additionally, we explore peptide-based materials for regulating metabolism and their potential synergic effect with other therapies, highlighting the mechanisms by which these peptides reverse drug resistance. Finally, we discuss future perspectives and the clinical challenges in peptide-based treatments, aiming to offer insights for overcoming drug-resistant diseases.

Comprehensive review of extraction, purification, structural characteristics, pharmacological activities, structure-activity relationship and application of seabuckthorn protein and peptides

Seabuckthorn (Hippophae rhamnoides) is an excellent plant that has the concomitant function of both medicine and foodstuff with high nutritional and health-promoting properties. As a pivotal bioactive component mainly existing in the seeds and leaves, seabuckthorn protein and its derived peptides have aroused wide attention owing to their multifaceted pharmacological activities, including anti-hypertensive, hypoglycemic, anti-obesity, anti-freeze, immunomodulatory, anti-inflammatory, sobriety, anti-oxidant and anti-neurodegenerative functions. Despite these promising attributes, the application of seabuckthorn peptides as functional food and medicines are impeded due to lack of a comprehensive understanding of pharmacological activities and intricate structure-activity relationship. Therefore, this review systematically summarizes the latest advancements in the extraction, purification, structural characteristics, pharmacological activities, digestion, absorption and transport, and application of seabuckthorn protein or peptides. Noteworthily, the structure-activity relationship is specifically delved into the hypoglycemic, anti-hypertensive, anti-obesity, anti-neurodegenerative and anti-oxidant peptides. Moreover, the shortcomings of current research and promising prospects are also highlighted. This comprehensive overview will provide a framework for future exploration and application of seabuckthorn protein or peptides in the realms of food and pharmaceuticals, offering a promising horizon for health benefits.

Natural biomaterials for sustainable flexible neuromorphic devices

Neuromorphic electronics use neural models in hardware to emulate brain-like behavior, and provide power-efficient, extremely compact, and massively-parallel processing, so they are ideal candidates for next-generation information-processing units. However, traditional rigid neuromorphic devices are limited by their unavoidable mechanical and geometrical mismatch with human tissues or organs. At the same time, the rapid development of these electronic devices has generated a large amount of electronic waste, thereby causing severe ecological problems. Natural biomaterials have mechanical properties compatible with biological tissues, and are environmentally benign, ultra-thin, and lightweight, so use of these materials can address these limitations and be used to create next-generation sustainable flexible neuromorphic electronics. Here, we explore the advantages of natural biomaterials in simulating synaptic behavior of sustainable neuromorphic devices. We present the flexibility, biocompatibility, and biodegradability of these neuromorphic devices, and consider the potential applicability of these properties in wearable and implantable bioelectronics. Finally, we consider the challenges of device fabrication and neuromorphic system integration by natural biomaterials, then suggest future research directions.

Interactions between pathological and functional amyloid: A match made in Heaven or Hell?

The amyloid state of proteins occurs in many different contexts in Nature and in modern society, ranging from the pathological kind (neurodegenerative diseases and amyloidosis) via man-made forms (food processing and - to a much smaller extent - protein biologics) to functional versions (bacterial biofilm, peptide hormones and signal transmission). These classes all come together in the human body which endogenously produces amyloidogenic protein able to form pathological human amyloid (PaHA), hosts a microbiome which continuously makes functional bacterial amyloid (FuBA) and ingests food which can contain amyloid. This can have grave consequences, given that PaHA can spread throughout the body in a "hand-me-down" fashion from cell to cell through small amyloid fragments, which can kick-start growth of new amyloid wherever they encounter monomeric amyloid precursors. Amyloid proteins can also self- and cross-seed across dissimilar peptide sequences. While it is very unlikely that ingested amyloid plays a role in this crosstalk, FuBA-PaHA interactions are increasingly implicated in vivo amyloid propagation. We are now in a position to understand the structural and bioinformatic basis for this cross-talk, thanks to the very recently obtained atomic-level structures of the two major FuBAs CsgA (E. coli) and FapC (Pseudomonas). While there are many reports of homology-driven heterotypic interactions between different PaHA, the human proteome does not harbor significant homology to CsgA and FapC. Yet we and others have uncovered significant cross-stimulation (and in some cases inhibition) of FuBA and PaHA both in vitro and in vivo, which we here rationalize based on structure and sequence. These interactions have important consequences for the transmission and development of neurodegenerative diseases, not least because FuBA and PaHA can come into contact via the gut-brain interface, recurrent infections with microbes and potentially even through invasive biofilm in the brain. Whether FuBA and PaHA first interact in the gut or the brain, they can both stimulate and block each other's aggregation as well as trigger inflammatory responses. The microbiome may also affect amyloidogenesis in other ways, e.g. through their own chaperones which recognize and block growth of both PaHA and FuBA as we show both experimentally and computationally. Heterotypic interactions between and within PaHA and FuBA both in vitro and in vivo are a vital part of the amyloid phenomenon and constitute a vibrant and exciting frontier for future research.

Unveiling the inhibition mechanism of host-defense peptide cathelicidin LL-37 on the amyloid aggregation of the human islet amyloid polypeptide

The aberrant aggregation of the human islet amyloid polypeptide (hIAPP) is a hallmark of type II diabetes. LL37, the only cathelicidin host-defense peptide in humans, plays essential roles in antimicrobial and immunomodulatory activities. Mounting evidence indicates that LL37 can inhibit the amyloid aggregation of hIAPP, suggesting possible interplays between infections and amyloid diseases while the mechanism remains unclear. In this paper, we explored the molecular interactions between hIAPP and LL37 using all-atom discrete molecular dynamics (DMD), a novel and predictive molecular dynamics engine with improved sampling efficiencies. We found that the LL37 peptides can effectively interact with hIAPP in monomer, oligomer, and fibril states driven by hydrophobic associations and pi-pi interactions. Specifically, the hydrophobic residues in the N- and C-termini of LL37 peptides can firmly bind with the monomeric and oligomeric hIAPP, especially in the amyloidogenic regions, to prevent the self-interactions of amyloidogenic regions and thus hinder the formation of amyloid fibrils. Furthermore, LL37 can bind to the elongation surfaces of the hIAPP fibril seeds with geometric incompatibility for monomer addition to block the fibril growth. Together, we identified the crucial residues and key driving forces for the interactions between LL37 and hIAPP peptides and revealed the related dynamics and conformational changes. The uncovered mechanism can contribute to a better understanding of the pathological links between microbial infections and amyloid diseases and guide the designs of novel therapies combining antimicrobial and anti-amyloid functions.

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Co-translational protein aggregation and ribosome stalling as a broad-spectrum antibacterial mechanism

Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with novel modes of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells, and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here, we describe an alternative mode of action that affects the same process: allowing translation to proceed but causing co-translational aggregation of the nascent peptidic chain. We show that treatment with an aggregation-prone peptide induces formation of polar inclusion bodies and activates the SsrA ribosome rescue pathway in bacteria. The inclusion bodies contain ribosomal proteins and ribosome hibernation factors, as well as mRNAs and cognate nascent chains of many proteins in amyloid-like structures, with a bias for membrane proteins with a fold rich in long-range beta-sheet interactions. The peptide is bactericidal against a wide range of pathogenic bacteria in planktonic growth and in biofilms, and reduces bacterial loads in mouse models of Escherichia coli and Acinetobacter baumannii infections. Our results indicate that disrupting protein homeostasis via co-translational aggregation constitutes a promising strategy for development of broad-spectrum antibacterials.

Emerging of Ultrafine Membraneless Organelles as the Missing Piece of Nanostress: Mechanism of Biogenesis and Implications at Multilevels

Understanding the interaction between nanomaterials and cellular structures is crucial for nanoparticle applications in biomedicine. We have identified a subtype of stress granules, called nanomaterial-provoked stress granules (NSGs), induced by gold nanorods (AuNRs). These NSGs differ from traditional SGs in their physical properties and biological functions. Uptake of AuNRs causes reactive oxygen species accumulation and protein misfolding in the cell, leading to NSG formation. Physically, NSGs have a gel-like core and a liquid-like shell, influenced positively by HSP70 and negatively by HSP90 and the ubiquitin-proteasome system. AuNRs promote NSG assembly by interacting with G3BP1, reducing the energy needed for liquid-liquid phase separation (LLPS). NSGs impact cellular functions by affecting mRNA surveillance and activating Adenosine 5'-monophosphate (AMP)-activated protein kinase signaling, crucial for a cellular stress response. Our study highlights the role of LLPS in nanomaterial metabolism and suggests NSGs as potential targets for drug delivery strategies, advancing the field of nanomedicine.

Functional classification of tauopathy strains reveals the role of protofilament core residues

Distinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells cause unique, transmissible neuropathology after inoculation. Strain amplification requires compatibility of the monomer and amyloid template. We used cryo-electron microscopy to study one cell-based yellow fluorescent protein (YFP)-tagged strain, resolving its amyloid nature. We then used sequential alanine (Ala) substitution (scan) within tau repeat domain (RD) to measure incorporation to preexisting tau RD-YFP aggregates. This robustly discriminated strains, defining sequences critical for monomer incorporation. We then created 3R/4R or 4R wild-type RD (amino acids 246 to 408) biosensors. Ala scan of recombinant tau seeds with the Alzheimer's disease (AD) fold matched that of AD homogenate. We scanned 22 brain lysates comprising four tauopathies. This clustered cases by neuropathological syndrome, revealed the role of amino acids in protofilament folds, and allowed strain discrimination based on amino acid requirements for prion replication.

Lipidic folding pathway of α-Synuclein via a toxic oligomer

Aggregation intermediates play a pivotal role in the assembly of amyloid fibrils, which are central to the pathogenesis of neurodegenerative diseases. The structures of filamentous intermediates and mature fibrils are now efficiently determined by single-particle cryo-electron microscopy. By contrast, smaller pre-fibrillar α-Synuclein (αS) oligomers, crucial for initiating amyloidogenesis, remain largely uncharacterized. We report an atomic-resolution structural characterization of a toxic pre-fibrillar aggregation intermediate (I1) on pathway to the formation of lipidic fibrils, which incorporate lipid molecules on protofilament surfaces during fibril growth on membranes. Super-resolution microscopy reveals a tetrameric state, providing insights into the early oligomeric assembly. Time resolved nuclear magnetic resonance (NMR) measurements uncover a structural reorganization essential for the transition of I1 to mature lipidic L2 fibrils. The reorganization involves the transformation of anti-parallel β-strands during the pre-fibrillar I1 state into a β-arc characteristic of amyloid fibrils. This structural reconfiguration occurs in a conserved structural kernel shared by a vast number of αS-fibril polymorphs including extracted fibrils from Parkinson's and Lewy Body Dementia patients. Consistent with reports of anti-parallel β-strands being a defining feature of toxic αS pre-fibrillar intermediates, I1 impacts viability of neuroblasts and disrupts cell membranes, resulting in an increased calcium influx. Our results integrate the occurrence of anti-parallel β-strands as salient features of toxic oligomers with their significant role in the amyloid fibril assembly pathway. These structural insights have implications for the development of therapies and biomarkers.

Multi-Site Red-Edge Excitation Shift Reveals the Residue-Specific Solvation Dynamics during the Native to Amyloid-like Transition of an Amyloidogenic Protein

Changes in water-protein interactions are crucial for proteins to achieve functional and nonfunctional conformations during structural transitions by modulating local stability. Amyloid-like protein aggregates in deteriorating neurons are hallmarks of neurodegenerative disorders. These aggregates form through significant structural changes, transitioning from functional native conformations to supramolecular cross-β-sheet structures via misfolded and oligomeric intermediates in a multistep process. However, the site-specific dynamics of water molecules from the native to misfolded conformations and further to oligomeric and compact amyloid structures remain poorly understood. In this study, we used the fluorescence method known as red-edge excitation shift (REES) to investigate the solvation dynamics at specific sites in various equilibrium conformations en route to the misfolding and aggregation of the functional domain of the TDP-43 protein (TDP-43tRRM). We generated three single tryptophan-single cysteine mutants of TDP-43tRRM, with the cysteines at different positions and tryptophan at a fixed position. Each sole cysteine was fluorescently labeled and used as a site-specific fluorophore along with the single tryptophan, creating four monitorable sites for REES studies. By investigating the site-specific extent of REES, we developed a residue-specific solvation dynamics map of TDP-43tRRM during its misfolding and aggregation. Our observations revealed that solvation dynamics progressively became more rigid and heterogeneous to varying extents at different sites during the transition from native to amyloid-like conformations.

Bioactive Deep Eutectic Solvent-Involved Sprayable Versatile Hydrogel for Monkeypox Virus Lesions Treatment

To address the issues of infectious virus, bacterial secondary infections, skin pigmentation, and scarring caused by monkeypox virus (MPXV), a sprayable hydrogel with versatile functions was developed with comprehensive properties. Based on current research, the bioactive deep eutectic solvent (DES) of rosmarinic acid-proanthocyanidin-glycol (RPG) was designed and synthesized as active agent, and molecular docking was applied to discover its binding to MPXV proteins through H-bonds and van der Waals interactions, and the docking results show the binding energies between RA, PC, Gly and MPXV proteins are -58.7188, -50.2311, and -18.4755 kcal/mol, respectively. Additionally, poly(vinyl alcohol) (PVA), borate, and xylitol (Xyl) were integrated with RPG to prepare the PB-RPG-Xyl hydrogel, which was characterized by popular ways. The pH-responsive properties of the hydrogel accelerated the release of RPG under acidic conditions, resulting in an increased cumulative release percentage of 84.83% at pH 5.5 at 210 min. Besides that, it was proved to have the expected sprayability, self-healing, adhesion, and shape-adaptability. The results of molecular dynamic simulation were meaningful to understanding its formation and self-healing mechanisms. Furthermore, the hydrogel shows ideal degradability, removability, and biocompatibility. Lastly, its multiple functions were systematically explored, including UV-blocking, blood clotting, cooling, antioxidant, antibacterial, and virus inhibition properties. The developed sprayable PB-RPG-Xyl hydrogel represents the first promising dressing based on natural bioactive DES for MPXV lesions management, which not only expands the application of green solvents in health care but also provides a convenient and effective treatment process for MPXV infection in the face of difficult skin lesions and complex treatment needs.

Strategic Modulation of Polarity and Viscosity Sensitivity of Bimane Molecular Rotor-Based Fluorophores for Imaging α-Synuclein

Molecular rotor-based fluorophores (RBFs) that are target-selective and sensitive to both polarity and viscosity are valuable for diverse biological applications. Here, we have designed next-generation RBFs based on the underexplored bimane fluorophore through either changing in aryl substitution or varying π-linkages between the rotatable electron donors and acceptors to produce red-shifted fluorescence emissions with large Stokes shifts. RBFs exhibit a twisted intramolecular charge transfer mechanism that enables control of polarity and viscosity sensitivity, as well as target selectivity. These features enable their application in: (1) turn-on fluorescent detection of α-synuclein (αS) fibrils, a hallmark of Parkinson's disease (PD), including amplified fibrils from patient samples; (2) monitoring early misfolding and oligomer formation during αS aggregation; and (3) selective imaging of αS condensates formed by liquid-liquid phase separation (LLPS). In all three cases, we show that our probes have high levels of selectivity for αS versus other aggregating proteins. These properties enable one to study the interplay of αS and tau in amyloid aggregation and the mechanisms underlying neurodegenerative disorders.

Advancing Alzheimer's Disease Modelling by Developing a Refined Biomimetic Brain Microenvironment for Facilitating High-Throughput Screening of Pharmacological Treatment Strategies

Alzheimer's disease (AD) poses a significant worldwide health challenge, requiring novel approaches for improved models and treatment development. This comprehensive review emphasises the systematic development and improvement of a biomimetic brain environment to address the shortcomings of existing AD models and enhance the efficiency of screening potential drug treatments. We identify drawbacks in traditional models and emphasise the necessity for more physiologically accurate systems through an in-depth analysis of current literature. This review aims to study the development of an advanced AD model that accurately replicates key AD pathophysiological aspects using cutting-edge biomaterials and microenvironment design. Incorporating biomolecular elements like Tau proteins and beta-amyloid (Aβ) plaques improve the accuracy of illustrating disease mechanisms. The expected results involve creating a solid foundation for high-throughput screening with enhanced scalability, translational significance, and the possibility of speeding up drug discovery. Thus, this review fills the gaps in AD modelling and shows potential for creating precise and efficient drug treatments for AD.

From Molecular to Radionuclide and Pharmacological Aspects in Transthyretin Cardiac Amyloidosis

Amyloidosis is a rare pathology characterized by protein deposits in various organs and tissues. Cardiac amyloidosis (CA) can be caused by various protein deposits, but transthyretin amyloidosis (ATTR) and immunoglobulin light chain (AL) are the most frequent pathologies. Protein misfolding can be induced by several factors such as oxidative stress, genetic mutations, aging, chronic inflammation, and neoplastic disorders. In ATTR cardiomyopathy (ATTR-CM), the amyloid fibrils can be found in the myocardium interstitial space and are associated with arrhythmias and heart failure. In pathological situations, the transthyretin (TTR) configuration is destroyed by proteolytic action, leading to monomers that further misfold and aggregate to form the amyloid fibrils. 99mTc-Pyrophosphate (99m-Tc-PYP), 99mTc 3,3-diphosphono-1,2-propanodicarboxylic acid (99m-Tc-DPD) and 99m-Tc hydroxy-methylene-Dyphosphonate (99m-Tc-HMDP) are used to detect myocardium amyloid deposits due to their ability to detect calcium ions that are present in the amyloid fibrils through dystrophic calcification. ATTR-CM therapy acts on different stages of the amyloidogenic process, including liver TTR synthesis, TTR tetramer destabilization, and misfolding of the monomers. The main aim of this narrative review is to present ATTR-CM, starting with molecular changes regarding the protein misfolding process and radionuclide aspects and finishing with pharmacological approaches.

Bioinformatics analysis and alternative polyadenylation in Heat Shock Proteins 70 (HSP70) family members

OBJECTIVE

The Heat Shock Protein 70 (HSP70) family is a highly conserved group of molecular chaperones essential for maintaining cellular homeostasis. These proteins are necessary for protein folding, assembly, and degradation and involve cell recovery from stress conditions. HSP70 proteins are upregulated in response to heat shock, oxidative stress, and pathogenic infections. Their primary role is preventing protein aggregation, refolding misfolded proteins, and targeted degradation of irreparably damaged proteins. Given their involvement in fundamental cellular processes and stress responses, HSP70 proteins are critical for cell survival and modulating disease outcomes in cancer, neurodegeneration, and other pathologies. The present study aims to understand domain architecture, physicochemical properties, phosphorylation, ubiquitination, and alternative polyadenylation site prediction in various HSP70 members.

METHOD

SMART and InterProScan software were used for domain analysis. EXPASY Protparam, NetPhos 3.1 server DTU, and MUbisiDa were used for physicochemical analysis, phosphorylation, and ubiquitination site analysis, respectively. Alternative polyadenylation was studied using the EST database.

RESULT

Domain analysis shows that coiled-coil and nucleotide-binding domains are present in some of the HSP70 members. Five HSP70 family members have alternate polyadenylation sites in their 3'UTR.

CONCLUSION

The present work has provided valuable insights into their structure, functions, interactome, and polyadenylation patterns. Studying their therapeutic potential in diseases like cancer can be helpful.

Beyond Misfolding: A New Paradigm for the Relationship Between Protein Folding and Aggregation

Aggregation is intricately linked to protein folding, necessitating a precise understanding of their relationship. Traditionally, aggregation has been viewed primarily as a sequential consequence of protein folding and misfolding. However, this conventional paradigm is inherently incomplete and can be deeply misleading. Remarkably, it fails to adequately explain how intrinsic and extrinsic factors, such as charges and cellular macromolecules, prevent intermolecular aggregation independently of intramolecular protein folding and structure. The pervasive inconsistencies between protein folding and aggregation call for a new framework. In all combined reactions of molecules, both intramolecular and intermolecular rate (or equilibrium) constants are mutually independent; accordingly, intrinsic and extrinsic factors independently affect both rate constants. This universal principle, when applied to protein folding and aggregation, indicates that they should be treated as two independent yet interconnected processes. Based on this principle, a new framework provides groundbreaking insights into misfolding, Anfinsen's thermodynamic hypothesis, molecular chaperones, intrinsic chaperone-like activities of cellular macromolecules, intermolecular repulsive force-driven aggregation inhibition, proteome solubility maintenance, and proteinopathies. Consequently, this paradigm shift not only refines our current understanding but also offers a more comprehensive view of how aggregation is coupled to protein folding in the complex cellular milieu.

Morpholine Anchored Fluorogenic Toolkit: Unveiled Disease Allied Protein Fibrillation in Lysosomal Compartment of Live-Cell and Drosophila Models

The aberrant accumulation of cytotoxic protein aggregates is a hallmark of various neurodegenerative and non-neurodegenerative ailments, necessitating the development of sensitive and selective tools for their detection. Herein, we report a series of morpholine-anchored fluorescent probes, denoted as SC-nmor (n = 2, 4, 6), designed for facile visualization of protein aggregates. These probes display notable changes in their photophysical properties upon binding with protein aggregates, owing to their high sensitivity to the fibrillar microenvironment. Specifically, the SC-4mor probe demonstrates strong selectivity for aggregated insulin proteins over native insulin, accompanied by a significant enhancement in fluorescence lifetime. Live-cell imaging reveals an exclusive localization at the lysosomal compartment. This feature enables the visualization of lysosomal accumulated protein fibrils induced with pepstatin A. Additionally, in vivo assessments on genetically mutated and dietary-modified Drosophila melanogaster, representing neurodegenerative and non-neurodegenerative disease models, demonstrate staining of protein aggregates. The enhanced emission from the eye lobes of Aβ-mutated and HSD brain samples, suggesting that SC-4mor can exhibit adequate retention in the brain with minimal biological toxicity. SC-4mor also shows its capability to cross the blood-brain barrier in mice model. Consequently, SC-4mor emerges as a promising marker for detecting and monitoring neurotoxic protein fibrillation in live cells and animal models, offering potential insights into the pathogenesis and progression of protein aggregation.

Dimethyl-Sulfoxide-Free Cell Cryoprotectant Derived from Amino Acids

With the large-scale applications of cryopreservation technology in the cell therapy fields, traditional permeable cryoprotectants (CPAs) have led to serious issues, such as cell cycle arrest, inhibition of cell proliferation and differentiation, apoptosis, altered gene expression, etc. Development of green, non-toxic cryoprotectants is critically needed. Amino acids could serve as substrates for protein and cellular metabolism and as cryoprotectants with non-toxicity, balancing the intracellular water osmotic pressure. Current research on amino acids as cryoprotectants is hindered by several limitations, including unclear protection mechanisms, cryopreservation methods, and poor efficacy of individual formulations. Therefore, three specific amino acids and derivatives, including l-proline, l-carnitine, and betaine, as cryoprotectants were used for two types of cell cryopreservation. Single-factor experiments were conducted to obtain the optimal concentration range for each of the three amino acid cryoprotectants. On the basis of the key thermophysical parameters, the ability to inhibit ice crystals, and the effect after cryopreservation, multivariate orthogonal experiments were carried out to evaluate the actual effect of the three-component mixed cryoprotectant on cell cryopreservation. In comparison to the gold standard of 10% dimethyl sulfoxide (DMSO) for cell cryopreservation, the mixed cryoprotectant derived from amino acids achieves comparable preservation efficacy at lower concentrations with a convenient application method, which offers guidance for DMSO-free cryoprotectants.

TAggiXL: A Fluorescence-Traceable Cross-Linking Strategy for Unbiased Profiling of Protein Aggregation and Interactome Dynamics

Protein aggregation is a hallmark of numerous degenerative diseases, yet its underlying mechanisms remain poorly understood due to the challenges in identifying the composition and interaction networks of these aggregates. To address this issue, we developed TAggiXL, a novel method that combines fluorescence-traceable aggregate isolation with cross-linking proteomics, significantly enhancing the efficiency and precision of isolating protein aggregates. This method facilitates unbiased profiling of aggregated proteomes and their interactomes in live cells. The TAggiXL approach leverages advanced cross-linking proteomics, density gradient centrifugation, and fluorescence tracking to provide detailed characterization of protein aggregation under various stress conditions including HSP90 and proteasome inhibition. Using TAggiXL, we identified key components and interactions within the aggregates, particularly highlighting E3 ubiquitin ligase TRIM26, which plays a crucial role in aggregate formation and autophagic clearance under stress and pathogenic conditions. Moreover, TAggiXL revealed that HSPA1B functions as a central interaction hub within the aggregated proteome. It preferentially interacts with intrinsically disordered regions (IDRs) of aggregate components and demonstrates dynamic behavior within the aggregate. In summary, TAggiXL offers a powerful tool for dissecting the complex composition and interaction networks of protein aggregates, with a significant potential to advance our understanding of protein aggregation in degenerative diseases. It also holds promise for the development of future therapeutic interventions.

Folding and Misfolding Dynamics of Irisin Protein Revealed by Single-Molecule Magnetic Tweezers

Irisin, a fibronectin III protein secreted by muscles during physical exercise, plays a significant role in the browning of white fat and cell adhesion, highlighting the importance of its conformational transitions. In this study, we investigated the folding and unfolding dynamics of a single irisin domain using a single-molecule manipulation technique known as magnetic tweezers. In addition to the native state, irisin can also fold transiently into a misfolded state. We determined the folding free energies of the native and misfolded states as well as their force-dependent folding and unfolding rates. The free energy of the misfolded state is higher than that of the unfolded state, and the misfolded state has a homogeneous force-dependent unfolding rate. The stable native state demonstrates heterogeneous unfolding rates that are within ∼1 order of magnitude. Via comparison with the well-studied 10th fibronectin III domain that has a partially folded intermediate state, our study demonstrates that proteins with similar structure can have distinct folding pathways.

Mitigating methylglyoxal-induced glycation stress: the protective role of iron, copper, and manganese coordination compounds in Saccharomyces cerevisiae

Glycation-induced stress (G-iS) is a physiological phenomenon that leads to the formation of advanced glycation end-products, triggering detrimental effects such as oxidative stress, inflammation, and damage to intracellular structures, tissues, and organs. This process is particularly relevant because it has been associated with various human pathologies, including cancer, neurodegenerative diseases, and diabetes. As therapeutic alternatives, coordination compounds with antioxidant activity show promising potential due to their versatility in attenuating oxidative stress and inflammation. Herein, we investigated the antioxidant-related protective potential of a series of complexes: [Cu(II)(BMPA)Cl2] (1), [Fe(III)(BMPA)Cl3] (2), and [Cl(BMPA)MnII-(μ-Cl)2-MnII(BMPA)-(μ-Cl)- MnII(BMPA)(Cl)2]•5H2O (3), all synthesized with the ligand bis-(2-pyridylmethyl)amine (BMPA) in Saccharomyces cerevisiae exposed to G-iS caused by methylglyoxal (MG). Pre- treatment with complexes 1-3 proved highly effective, increasing yeast tolerance to G-iS and attenuating mitochondrial dysfunction. This observed phenotype appears to result from a reduction in intracellular oxidation, lipid peroxidation levels, and glycation. Additionally, an increase in the activity of the antioxidant enzymes superoxide dismutase and catalase was observed following treatment with complexes 1-3. Notably, although complexes 1-3 provided significant protection against oxidative stress induced by H2O2 and menadione, their protective role was more effective against MG-induced glycation stress. Our results indicate that these complexes possess both antiglycation and antioxidant properties, warranting further investigation as potential interventions for mitigating glycation and oxidative stress-related pathologies.

Amyloid-Driven Allostery

The fields of allostery and amyloid-related pathologies, such as Parkinson's disease (PD), have been extensively explored individually, but less is known about how amyloids control allostery. Recent advancements have revealed that amyloids can drive allosteric effects in both intrinsically disordered proteins, such as alpha-synuclein (αS), and multi-domain signaling proteins, such as protein kinase A (PKA). Amyloid-driven allostery plays a central role in explaining the mechanisms of gain-of-pathological-function mutations in αS (e.g. E46K, which causes early PD onset) and loss-of-physiological-function mutations in PKA (e.g. A211D, which predisposes to tumors). This review highlights allosteric effects of disease-related mutations and how they can cause exposure of amyloidogenic regions, leading to amyloids that are either toxic or cause aberrant signaling. We also discuss multiple potential modulators of these allosteric effects, such as MgATP and kinase substrates, opening future opportunities to improve current pharmacological interventions against αS and PKA-related pathologies. Overall, we show that amyloid-driven allosteric models are useful to explain the mechanisms underlying disease-related mutations.

Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation

Emerging evidence suggests that physiological C-terminal truncation of α-synuclein (αS) plays a critical role in regulating liquid-liquid phase separation and promoting amyloid aggregation, processes implicated in neurodegenerative diseases such as Parkinson's disease (PD). However, the molecular mechanisms through which C-terminal truncation influences αS conformation and modulates its aggregation remain poorly understood. In this study, we investigated the impact of C-terminal truncation on αS conformational dynamics by comparing full-length αS1-140 with truncated αS1-103 monomers using atomistic discrete molecular dynamics simulations. Our findings revealed that both αS1-140 and αS1-103 primarily adopted helical conformations around residues 7-32, while residues 36-95, located in the second half of the N-terminal and NAC domains, predominantly formed a dynamic β-sheet core. The C-terminus of αS1-140 was largely unstructured and dynamically wrapped around the β-sheet core. While residues 1-95 exhibited similar secondary structure propensities in both αS1-140 and αS1-103, the dynamic capping by the C-terminus in αS1-140 slightly enhanced β-sheet formation around residues 36-95. In contrast, key aggregation-driving regions (residues 2-9, 36-42, 45-57, and 68-78) were dynamically shielded by the C-terminus in αS1-140, reducing their exposure and potentially preventing interpeptide interactions that drive aggregation. C-terminal truncation, on the other hand, increased the exposed surface area of these aggregation-prone regions, thereby enhancing interpeptide interactions, phase separation, and amyloid aggregation. Overall, our simulations provide valuable insights into the conformational effects of C-terminal truncation on αS and its role in promoting pathological aggregation.

Designed Cell-Penetrating Peptide Constructs for Inhibition of Pathogenic Protein Self-Assembly

Peptides possess a number of pharmacologically desirable properties, including greater chemical diversity than other biomolecule classes and the ability to selectively bind to specific targets with high potency, as well as biocompatibility, biodegradability, and ease and low cost of production. Consequently, there has been considerable interest in developing peptide-based therapeutics, including amyloid inhibitors. However, a major hindrance to the successful therapeutic application of peptides is their poor delivery to target tissues, cells or subcellular organelles. To overcome these issues, recent efforts have focused on engineering cell-penetrating peptide (CPP) antagonists of amyloidogenesis, which combine the attractive intrinsic properties of peptides with potent therapeutic effects (i.e., inhibition of amyloid formation and the associated cytotoxicity) and highly efficient delivery (to target tissue, cells, and organelles). This review highlights some promising CPP constructs designed to target amyloid aggregation associated with a diverse range of disorders, including Alzheimer's disease, transmissible spongiform encephalopathies (or prion diseases), Parkinson's disease, and cancer.

Innovative synthesis and molecular modeling of actinomycetes-derived silver nanoparticles for biomedical applications

The rising demand for innovative antimicrobial solutions has shifted focus towards silver nanoparticles (AgNPs), especially those produced through eco-friendly methods. This study introduces a novel approach utilizing actinomycetes strains-Streptomyces albus, Micromonospora maris, and Arthrobacter crystallopoietes-to biosynthesize AgNPs with remarkable antibacterial properties. Through molecular characterization, we identified unique features of these nanoparticles, and computational modeling suggested significant ion-ligand interactions with proteins 6REV and 3K07. Our research highlights the promise of these biogenically synthesized nanoparticles in advancing biomedical applications. Actinomycetes were sourced and screened for their ability to produce metallic nanoparticles, revealing that among 35 samples, only six showed this capability. Notably, Streptomyces albus strain smmdk14 (OR685674), Micromonospora maris strain smmdk13 (OR685672), and Arthrobacter crystallopoietes strain smmdk12 (OR685674) were identified as effective silver nanoparticle producers. The synthesized nanoparticles demonstrated potent antibacterial activity against common pathogens including E. coli, Pseudomonas aeruginosa, Klebsiella spp., Enterococcus faecalis, Staphylococcus aureus, and Acinetobacter spp. The data obtained from color change observation, UV-visible spectrophotometry, Zeta potential, FTIR spectroscopy, and transmission electron microscopy (TEM) characterized AgNPs potentiality. The nanoparticles were spherical, with sizes ranging from 6.46 nm to 24.7 nm. Optimization of production conditions, comparison of antimicrobial effects with antibiotics, evaluation of potential toxicity, and assessment of wound-healing capabilities were also conducted. The biosynthesized AgNPs exhibited superior antibacterial properties compared to traditional antibiotics and significantly accelerated wound healing by approximately 66.4 % in fibroblast cell cultures. Additionally, computational analysis predicted interactions between various metal ions and specific amino acid residues in proteins 6REV and 3K07. Overall, this study demonstrates the successful creation of AgNPs with notable antibacterial and wound-healing properties, underscoring their potential for medical applications.

Structural and Functional Relevance of Charge Based Transient Interactions inside Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) perform a wide range of biological functions without adopting stable, well-defined, three-dimensional structures. Instead, IDPs exist as dynamic ensembles of flexible conformations, traditionally thought to be governed by weak, nonspecific interactions, which are well described by homopolymer theory. However, recent research highlights the presence of transient, specific interactions in several IDPs, suggesting that factors beyond overall size influence their conformational behavior. In this study, we investigate how the spatial arrangement of charged amino acids within IDP sequences shapes the prevalence of transient, specific interactions. Through a series of model peptides, we establish a quantitative empirical relationship between the fraction of transient interactions and a novel sequence metric, termed effective charged patch length, which characterizes the ability of charged patches to drive these interactions. By examining IDP ensembles with varying levels of transient interactions, we further explore their heteropolymeric structural behavior in phase-separated condensates, where we observe the formation of a condensate-spanning network structure. Additionally, we perform a proteome-wide scan for charge-based transient interactions within disordered regions of the human proteome, revealing that approximately 10% of these regions exhibit such charge-driven transient interactions, leading to heteropolymeric behaviors in their conformational ensembles. Finally, we examine how these charge-based transient interactions correlate with molecular functions, identifying specific biological roles in which these interactions are enriched.

COCOMO2: A coarse-grained model for interacting folded and disordered proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parameterized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multi-scale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Real-Time Visualization of Protein Microenvironment Changes with High Spatial Resolution in Live Cells via Site-Specific Incorporation of Rotor-Based Fluorescent Noncanonical Amino Acids

Traditional methods, such as the use of fluorescent protein fusions and environment-sensitive fluorophores, have limitations when studying protein microenvironment changes at the finest spatial resolution. These techniques often rely on bulky proteins or tags restricted to the N- or C-terminus, which can disrupt the natural behavior of the target protein and dramatically limit the ability of their method to investigate noninvasively microenvironment effects. To overcome these challenges, we have developed an innovative strategy to visualize microenvironment changes of protein substructures in real-time by genetically incorporating environment-sensitive noncanonical amino acids (ncAAs) containing rotor-based fluorophores (RBFs) at specific positions within a protein of interest. Through computational redesign of aminoacyl-tRNA synthetase, we successfully incorporated these rotor-based ncAAs into various proteins in mammalian cells. By site-specifically placing these ncAAs in distinct regions of proteins, we detected microenvironmental changes of several different protein domains during events such as aggregation, clustering, aggregation disassembly, and cluster dissociation.

Cardiac Amyloidosis: State-of-the-Art Review in Molecular Pathology

Amyloidosis refers to a group of diseases caused by extracellular deposits of misfolded proteins, which alter tissue function and structure, potentially affecting any organ. The term "amyloid" was introduced in the 19th century and later associated with pathological protein deposits. Amyloid fibrils, which are insoluble and resistant to degradation, originate from soluble proteins that undergo misfolding. This process can be triggered by several factors, such as aging, elevated protein concentrations, or pathogenic variants. Amyloid deposits damage organs both by disrupting tissue architecture and through direct cytotoxic effects, leading to conditions such as heart failure. Amyloidosis can be classified into acquired or inherited forms and can be systemic or localized. Diagnosing cardiac amyloidosis is complex and often requires tissue biopsies, which are supported by Congo Red dye staining. In some cases, bisphosphonate bone scans may provide a less invasive diagnostic option. In this state-of-the-art review, we focus on the most common forms of cardiac amyloidosis, from epidemiology to therapy, emphasizing the differences in molecular mechanisms and the importance of pathological diagnosis for appropriate treatment using a multidisciplinary approach.

The essential role of CCT2 in the regulation of aggrephagy

Protein aggregation, a defining characteristic of numerous human diseases, poses a significant challenge to cellular health. Autophagy, an essential cellular recycling process, specifically targets and degrades these harmful protein aggregates through a specialized mechanism known as aggrephagy. However, the precise mechanisms underlying the exquisite selectivity of aggrephagy in identifying and eliminating only aggregated proteins while sparing healthy cellular components have remained enigmatic. Here, in this mini review, we highlights the essential role of CCT2, a subunit of the chaperonin TRiC complex, in regulating aggrephagy. CCT2, traditionally viewed as a molecular chaperone, has emerged as a novel autophagy receptor that specifically targets solid protein aggregates for degradation. This ubiquitination-independent mode of recognition by CCT2 expands our understanding of protein degradation pathways. The functional switch of CCT2 from a chaperone to an autophagy receptor underscores its dynamic nature and ability to adapt to cellular stress. The selectivity of CCT2-mediated aggrephagy for solid aggregates has implications for neurodegenerative diseases. Further research is warranted to explore the therapeutic potential of enhancing CCT2-mediated aggrephagy in such diseases.

Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots

In classical amyloidoses, amyloid fibres form through the nucleation and accretion of protein monomers, with protofibrils and fibrils exhibiting a cross-β motif of parallel or antiparallel β-sheets oriented perpendicular to the fibre direction. These protofibrils and fibrils can intertwine to form mature amyloid fibres. Similar phenomena can occur in blood from individuals with circulating inflammatory molecules (and also some originating from viruses and bacteria). Such pathological clotting can result in an anomalous amyloid form termed fibrinaloid microclots. Previous proteomic analyses of these microclots have shown the presence of non-fibrin(ogen) proteins, suggesting a more complex mechanism than simple entrapment. We thus provide evidence against such a simple entrapment model, noting that clot pores are too large and centrifugation would have removed weakly bound proteins. Instead, we explore whether co-aggregation into amyloid fibres may involve axial (multiple proteins within the same fibril), lateral (single-protein fibrils contributing to a fibre), or both types of integration. Our analysis of proteomic data from fibrinaloid microclots in different diseases shows no significant quantitative overlap with the normal plasma proteome and no correlation between plasma protein abundance and their presence in fibrinaloid microclots. Notably, abundant plasma proteins like α-2-macroglobulin, fibronectin, and transthyretin are absent from microclots, while less abundant proteins such as adiponectin, periostin, and von Willebrand factor are well represented. Using bioinformatic tools, including AmyloGram and AnuPP, we found that proteins entrapped in fibrinaloid microclots exhibit high amyloidogenic tendencies, suggesting their integration as cross-β elements into amyloid structures. This integration likely contributes to the microclots' resistance to proteolysis. Our findings underscore the role of cross-seeding in fibrinaloid microclot formation and highlight the need for further investigation into their structural properties and implications in thrombotic and amyloid diseases. These insights provide a foundation for developing novel diagnostic and therapeutic strategies targeting amyloidogenic cross-seeding in blood clotting disorders.

Intrinsic conformational preference in the monomeric protein governs amyloid polymorphism

The inherent stochasticity associated with the hierarchical self-assembly of either native-like or partially-unfolded protein monomers leads to the formation of transient, morphologically-diverse prefibrillar species resulting in structurally-distinct polymorphic protein aggregates. High-resolution structural characterization of mature aggregates has revealed heterogeneous supramolecular packing of protofibrils within amyloid polymorphs. However, little is known about whether initial monomeric protein conformers engender polymorphism at the onset of aggregation. Here, we show that intrinsic conformational preference in aggregation-competent monomeric ovalbumin, an archetypal serpin, dictates fibrillar polymorphism by modulating aggregation pathways. Using fluorescence, FT-IR, and vibrational Raman spectroscopy coupled with dynamic light scattering and electron microscopy, we demonstrate that conformationally-diverse amyloidogenic monomers, formed via an interplay of electrostatic and hydrophobic interactions before the commencement of aggregation, play a crucial role in promoting amyloid polymorphism. Moreover, the monomeric conformational fingerprints, accrued at the onset of aggregation, persist and propagate during the formation of polymorphic amyloids. Our results delineate essential conformational characteristics of the monomeric protein preceding aggregation, which will have broad implications in the mechanistic understanding of amyloid strain diversity observed in disease-related proteins.

Native State Stabilization of Amyloidogenic Proteins by Kinetic Stabilizers: Inhibition of Protein Aggregation and Clinical Relevance

Proteinopathies or amyloidoses are a group of life-threatening disorders that result from misfolding of proteins and aggregation into toxic insoluble amyloid aggregates. Amyloid aggregates have low clearance from the body due to the insoluble nature, leading to their deposition in various organs and consequent organ dysfunction. While amyloid deposition in the central nervous system leads to neurodegenerative diseases that mostly cause dementia and difficulty in movement, several other organs, including heart, liver and kidney are also affected by systemic amyloidoses. Regardless of the site of amyloid deposition, misfolding and structural alteration of the precursor proteins play the central role in amyloid formation. Kinetic stabilizers are an emerging class of drugs, which act like pharmacological chaperones to stabilize the native state structure of amyloidogenic proteins and to increase the activation energy barrier that is required for adopting a misfolded structure or conformation, ultimately leading to the inhibition of protein aggregation. In this review, we discuss the kinetic stabilizers that stabilize the native quaternary structure of transthyretin, immunoglobulin light chain and superoxide dismutase 1 that cause transthyretin amyloidoses, light chain amyloidosis and familial amyotrophic lateral sclerosis, respectively.