protein folding

Improvement of functional and antioxidant properties of Sacha inchi protein through glycosylation with chitosan oligosaccharide

Comprehensive analysis of non-synonymous single-nucleotide polymorphism of human TSC1 and TSC2 genes: An in silico approach

Abstract Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by mutations in the TSC1 and TSC2 genes and is characterized by benign hamartoma formation in multiple organs. The TSC1–TSC2 complex regulates mTORC1 signaling in response to cellular growth conditions. This study aims to predict the structural stability and functional effects of non-synonymous single-nucleotide polymorphisms (nsSNPs) in human TSC1 and TSC2 using computational approaches. Twelve computational tools were assessed using receiver operating characteristic (ROC) analysis and applied to identify deleterious nsSNPs. Protein stability was predicted using I-Mutant 2.0 and MUpro, while evolutionary conservation was analyzed with ConSurf. NetPhos 3.1 identified potential PTM sites, and MutPred2.0 evaluated their functional impact. Project HOPE assessed mutation-induced physicochemical changes. Structural models were validated using multiple tools, visualized in ChimeraX 1.9, and further evaluated by molecular dynamics simulation to confirm wild-type and mutant stability. All twelve tools had AUC values above 0.90. A combined in silico analysis identified twelve high-risk nsSNPs in TSC1 and sixteen in TSC2, all reducing protein stability, located in conserved regions, and potentially disrupting phosphorylation sites. MutPred and Project HOPE confirmed their impact on protein function. Functional analysis showed TSC1 and TSC2 affect mTORC1 and PI3K–Akt pathways. RMSF and RMSD analyses revealed that TSC1 variants rs1846545280 (G236E), and rs2132135678 (V234E), and TSC2 variants rs45517223 (S758C), rs2151354925 (T836P), and rs45517365 (R1570W) had the largest structural fluctuations. Substitution with glutamic acid, a negatively charged and bulkier residue, may disrupt local folding of TSC1. Similarly, replacement of arginine with tyrosine at position 1570 may impair Rheb binding at the GAP domain of TSC2. These findings highlight potentially pathogenic nsSNPs in TSC1 and TSC2.

Discovery and Characterization of a Novel Ligand-Binding Site in UFC1 Using Sulfa- and Sulfonate-Based Compounds

Abstract UFMylation is an important biological process where proteins are post-translationally modified via the covalent attachment of the ubiquitin-like modifier (UBL), ubiquitin-fold modifier-1 (UFM1). UFMylation is analogous to ubiquitination, occurring via the transfer of UFM1 across E1-, E2-, and E3-like enzymes, represented by ubiquitin-like modifier-activating enzyme 5 (UBA5), ubiquitin-fold modifier conjugating enzyme 1 (UFC1), and UFM1-specific ligase 1 (UFL1), respectively. Recent work has shown that dysregulation of UFMylation is associated with several diseases, sparking interest in characterizing its enzymes as potential drug targets. To date, only inhibitors targeting UBA5 have been identified, but no such ligands exist for UFC1. In this study, we present the structure of UFC1 in complex with the sulfonic acid CAPS, which revealed a novel ligand-binding pocket in UFC1. Using biophysical assays, coupled with X-ray crystallographic studies of UFC1 variants, we show that binding of CAPS to UFC1 appears pH-dependent and is enhanced by Tyr42. Further, our TSA data show that other sulfa- and sulfonate-based compounds induce dose-dependent destabilization of UFC1, consistent with weak but direct interactions with the enzyme. Lastly, using a UFMylation assay, we show that CAPS, along with Tyr42, may have a limited influence on UFM1 transfer to UFC1 and, consequently, downstream UFMylation of protein substrates. Nevertheless, our data indicate that the CAPS-binding pocket may serve as a design scaffold for the development of UFC1 modulators. With UFC1 emerging as a drug target, our study provides a possible avenue for the design and development of novel UFC1-specific modulators with therapeutic potential.

Image-based and biochemical multimodal phenotyping for explainable classification of chia (Salvia hispanica L.) genotypes.

The findings indicate that multimodal phenotyping, coupled with explainable machine learning, offers a practical and biologically interpretable decision-support approach for chia genotype classification.

Soy Protein Isolate-β-Cyclodextrin Microencapsulation Boosts Stability and Intestinal Delivery of α-Linolenic Acid-Rich Structured Lipids: Oxidation, Digestion, and Molecular Docking Evaluation.

In vitro simulated digestion demonstrated its characteristic intestinal sustained-release behavior, which provides preliminary in vitro evidence that may favor enhanced intestinal absorption of α-linolenic acid (ALA); however, further cellular or animal trials are required to quantitatively validate its actual in vivo bioavailability improvement.

β-strand addition within tip initiation complexes licenses assembly of diverse type IV filaments

How PilC/PilY1 can be retained on the fiber tip under enormous tensile loads generated during mechanical shear and T4P retraction is explained and how diverse T4P systems employ β-strand addition to license fiber assembly is demonstrated.

Leveraging Protein Dynamics for Selective Inhibition of Threonyl-tRNA Synthetase by Obafluorin Analogs.

A structure dynamics-based design strategy is reported that transforms OB into a selective antibacterial agent through rational modification of the nitrophenyl moiety, and establishes a 'kinetic sensor' strategy for achieving species selectivity.

A hydrogel microsphere-based catalytic hairpin assembly for simple miRNA detection.

A hydrogel microsphere-based CHA method that integrates CHA signal amplification with the solid-phase carrier of hydrogel microspheres for the detection of miRNAs in blood samples with favorable application potential for the detection of miRNA biomarkers in complex biological samples with a simple, low-cost, enzyme-free mode is reported.

Prevalence of Vitamin D Deficiency and Its Association with Disease Activity among Libyan Patients with Inflammatory Bowel Disease

Suboptimal vitamin D status is highly prevalent among IBD patients in Misurata, Libya, with disease activity acting as the primary driver of vitamin D depletion regardless of patient gender, underscoring the critical need for continuous assessment and the implementation of effective supplementation strategies to improve therapeutic outcomes across all IBD cohorts.

Local Frustration Modulates the Folding Dynamics of a Repeat Protein

Repeat proteins fold through pathways that are strongly shaped by local energetics, making them highly sensitive to mutations. The ankyrin repeat (AR) domain of IκBα is a cooperative folding unit in which the first four repeats (AR1–AR4) are stable, while the last two are destabilized. Despite this simple modular architecture, IκBα follows a complex folding trajectory involving high-energy intermediates. Here, we investigate how sequence variations modulate folding pathways using coarse-grained AWSEM simulations combined with the Energy Landscape Visualization Method (ELViM) and local frustration analysis. We compare the wild type (WT) with two consensus-designed variants: V93L, which accelerates folding, and L131V, which destabilizes and slows down folding of the protein in vitro. Our results show that WT and V93L share a similar folding funnel, though V93L folds more directly into the native state. In contrast, L131V reshapes the landscape by stabilizing non-native kinetic trap with minimally frustrated contacts. Reversing the L131V mutation allows the protein to reach the native conformation, whereas maintaining it confines the protein to misfolded states that can only be escaped at very high temperatures, without productive folding. These findings highlight how subtle sequence changes can tune frustration, modulate kinetic trapping, and control folding efficiency in repeat proteins.

Title: Temporal Wave Function Collapse Dynamics

Temporal Wave Function Collapse Dynamics explores the theoretical underpinnings of the collapse of temporal wave functions – fundamental units of information within complex systems such as neural networks and protein folding – as a dynamic process. This paper posits that collapse isn't a discrete event but rather a continuous evolution driven by a set of differential equations that capture the interplay between system state, external stimuli, and feedback loops. We propose a novel differential equation system that models this collapse, emphasizing the generation of new, potentially transformative states. This research aims to advance our understanding of complex system behavior by providing a framework for modeling this fundamental process.

Aortic disease-linked mutations reveal unexpected convergent allosteric mechanisms of protein kinase G misregulation

Thoracic aortic aneurysms and dissections (TAAD) are life-threatening conditions linked to gain-of-function mutations in cGMP-dependent protein kinase I (PKG I), a central regulator of vascular smooth muscle signaling. Among these, substitutions at Val 234 have been associated with kinase overactivation and early-onset disease, despite this residue being distal from the active site and cGMP binding regions. Using NMR, molecular dynamics simulations, and complementary kinase and binding assays, we show that Val 234 acts as a crucial allosteric hub of PKG autoinhibition. TAAD-associated variants at Val 234 disrupt PKG regulation through two distinct yet complementary allosteric mechanisms: by biasing the kinase toward active conformations that increase sensitivity to cGMP and by decreasing the folding stability of the regulatory domain, thereby weakening inhibitory contacts independently of cGMP control. Despite these differences, both mechanisms result in excessive PKG signaling at basal and intermediate cGMP levels, while maximal activity remains unaltered. Together, these findings explain how distal mutations can unpredictably rewire kinase allostery and drive pathogenic vascular signaling.