Although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (IUPs) remain to be elucidated. This review is focused on the...
Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of...
Polypeptide polymers can adopt natural protein secondary structures such as α-helices or β-sheets, and this unique feature is at the origin of some intriguing physico–chemical properties. In this work, we present how side chain imidazoylation of a po...
Random walks (RWs) have been important in statistical physics and can describe the statistical properties of various processes in physical, chemical, and biological systems. In this study, we have proposed a self-interacting random walk model in a co...
Human SNF5 and BAF155 constitute the core subunit of multi-protein SWI/SNF chromatin-remodeling complexes that are required for ATP-dependent nucleosome mobility and transcriptional control. Human SNF5 (hSNF5) utilizes its repeat 1 (RPT1) domain to a...
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
We review a general framework of pressure effects on the structures formed by entropically driven self-assembly (for example, denaturation of proteins from their native structure and dissociation of ordered structure of the amyloid fibril occur at hi...
Within the recently developed Hamiltonian formulation of the Zimm and Bragg model we re-evaluate several size dependent approximations of model partition function. Our size analysis is based on the comparison of chain length N with the maximal correl...
Fast kinetic experiments with dramatically improved time resolution have contributed significantly to understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpin, contact formation, and overa...
Reduced-molar-mass low-acyl gellan gum was obtained by the centrifugation of an aqueous solution of commercially available food-grade gellan gum. The derived sample was characterized by NMR, FTIR, ICPE, and viscometry methods. The characteristics wer...
We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation t...
The toxicity of botulinum multi-domain neurotoxins (BoNTs) arises from a sequence of molecular events, in which the translocation of the catalytic domain through the membrane of a neurotransmitter vesicle plays a key role. A recent structural study o...
Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly α-helical structure. We tes...
The effects of proline co-solvent on helix folding are explored through the single discrete coordinate of the number of helical hydrogen bonds. The analysis is based on multi-microsecond length molecular dynamics simulations of alanine-based helix-fo...
This paper presents an analysis of the effect of the geometry of the end-coil transition zone on the material stress state of a machined compression spring with a rectangular wire cross-section. The literature relationships for determining the stress...
We present an analysis of α-helix folding in the coarse-grained coordinate of number of formed helical hydrogen bonds (NHBs) for four alanine peptides (ALA)n, with n = 5, 8, 15, and 21 residues. Starting with multi-microsecond all-atom molecula...
The bacterial flagellar motor consists of a rotor and stator units and is driven by ion flow through the stator. The activation of the ion flow is coupled with the anchoring of the stator units to the peptidoglycan layer by the stator B-subunit aroun...
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic ins...
Protein/Peptide amyloidosis is the main cause of several diseases, such as neurodegenerative diseases. It has been widely acknowledged that the unnatural fibrillation of protein/peptides in vivo is significantly affected by the physical and chemical...
The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c′, were detected by a small-angle neutron scattering experiment (SANS). The struct...
The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or ra...
To promote the transition to a cleaner energy structure and support the achievement of the “carbon peak and carbon neutrality” goals, concentrated solar power (CSP) technology has attracted increasing attention. The molten salt globe valv...
In order to reduce chronic hair flyaways/frizz, both reducing and oxidizing agents have to be used, leaving aside the hair damage issues. This study presents changes in hair morphology caused by treatment with a shampoo containing only reducing agent...
Gelling carrageenans are polysaccharides extracted from the Gigartinales order of red algae. These are additives used essentially in the food industry for texturizing, stabilizing or gelling various formulations. Although a consensual gel mechanism h...
In this study, we fed the larval of Bombyx mori silkworms with nanodroplets of liquid metal (LM) coated with microgels of marine polysaccharides to obtain stretchable silk. Alginate-coated liquid metal nanodroplets (LM@NaAlg) were prepared with signi...
The release of flavor compounds is a critical factor that influences the quality of fermented foods. A recent study investigated the interactions between four fermentation-stinky compounds (indole, isovaleric acid, dimethyl disulfide, and dibutyl pht...
16 December 2024
Xanthan gum (XG) is a well-known anionic polysaccharide that finds broad application in the food and petroleum industries because of its ability to enhance solution viscosity at low concentrations and moderate temperatures. The aim of this work was t...
In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quart...
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuat...
Self-assembled fibrillation of wheat gluten is a common phenomenon in the daily production and processing of wheat flour products. The driving forces for its formation and the factors that influence the morphology of fibrils have not been thoroughly...
Cytochrome c is one of the most prominent representatives of peripheral membrane proteins. Besides functioning as an electron transfer carrier in the mitochondrial respiratory chain, it can acquire peroxidase capability, promote the self-assembly of...
Plant-based proteins offer sustainable alternatives to animal sources, yet their lower digestibility remains a critical barrier to widespread applications. Current digestibility assessment methods require days of analysis and gram-scale samples, crea...
The aim of this study was to characterize the collagens from the body of surf clam shell (Coelomactra antiquata). Guanidine hydrochloride and pepsin were used to extract collagens. Guanidine hydrochloride soluble collagen (GSC) and pepsin soluble col...
Dermaseptins belonging to a large family of cationic membrane-disruption antimicrobial peptides display extensive antibacterial and antiproliferative activities depending on a coil-to-helix transition and the specific structural parameters. Herein, a...
This study employed a multi-technique approach to investigate the structural and conformational changes in proteins in Meretrix lyrata (M. lyrata) adductor, foot, and siphon tissues during boiling. Data-independent acquisition (DIA) quantitative prot...
The skin of yellowfin tuna is one of the fishery industry solid residues with the greatest potential to add extra value to its circular economy that remains yet unexploited. Particularly, the high collagen content of fish skin allows generating gelat...
Chiba tofu is a new type of vegetarian food prepared with soy protein isolate (SPI). According to factory feedback, the SPI stored in the factory storeroom in summer undergoes reactive oxidation, which changes the structure of SPI and further affects...
The polypeptide Nisin is characterized by antibacterial properties, making it a compound with many applications, mainly in the food industry. As a result, a deeper understanding of its behaviour, especially after its dissolution in water, is of the u...
Cold environments challenge the structural and functional integrity of membrane proteins, requiring specialized adaptations to maintain activity under low thermal energy. Here, we investigate the molecular basis of cold tolerance in the peptide trans...
Wooden breast myopathy (WBM) is a meat abnormality affecting pectoralis majors (PMs) of fast-growing broiler chickens. WBM-affected PMs exhibited varied meat qualities with increasing WBM severity. Normal PMs (NOR), mild WBM-affected PMs (MIL), moder...
Ca2+/calmodulin (Ca2+/CaM) interaction with connexins (Cx) is well-established; however, the mechanistic basis of regulation of gap junction function by Ca2+/CaM is not fully understood. Ca2+/CaM is predicted to bind to a domain in the C-terminal por...