Atomistic Simulation of Water Incorporation and Mobility in Bombyx mori Silk Fibroin

Nanoscale self-assembly and water retention properties of silk fibroin-riboflavin hydrogel

Silk-fibroin hydrogels have gained considerable attention in recent years for their versatile biomedical applications. The physical properties of a complex hydrogel, comprising silk fibroin and riboflavin, surpass those of the silk fibroin-hydrogel without additives. This study investigates silk fibroin-riboflavin (silk-RIB) hydrogel at the atomistic level to uncover molecular structures and chemical characteristics specific to silk fibroin and riboflavin molecules in an aqueous medium. The interplay between hydrophilic riboflavin and hydrophobic silk fibroin polymers facilitates the formation of solubilized silk fiber, which subsequently evolves into a nano-scale hydrogel over time. Eventually, the interlinked RIB stacks form a scaffold that not only accommodates silk fibroin aggregates but also encloses water pockets, preserving the moisture level and enhancing the thermal conductivity of the hydrogel. To explore water retention properties and the role of ions, two sets of simulations of semi-hydrated hydrogel in the presence and absence of ions are conducted. The presence of ions significantly influences the dynamics of RIB and silk fibroin. Favorable interactions with the ions impede the unrestricted diffusion of these larger molecules, potentially leading to a stable structure capable of retaining water for a prolonged duration. The complete removal of water results in further shrinkage of the anhydrous silk-RIB hydrogel or xerogel (XG), yet its porosity and structural integrity remain intact. These findings offer valuable insights into the behavior of silk fibroin hydrogel and XG, paving the way for materials engineering in aqueous environments to develop biomedical devices with customized functional properties.

The Impact of Temperature and Pressure on the Structural Stability of Solvated Solid-State Conformations of Bombyx mori Silk Fibroins: Insights from Molecular Dynamics Simulations

Bombyx mori silk fibroin is a promising biopolymer with notable mechanical strength, biocompatibility, and potential for diverse biomedical applications, such as tissue engineering scaffolds, and drug delivery. These properties are intrinsically linked to the structural characteristics of silk fibroin, making it essential to understand its molecular stability under varying environmental conditions. This study employed molecular dynamics simulations to examine the structural stability of silk I and silk II conformations of silk fibroin under changes in temperature (298 K to 378 K) and pressure (0.1 MPa to 700 MPa). Key parameters, including Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of Gyration (Rg) were analyzed, along with non-bonded interactions such as van der Waals and electrostatic potential energy. Our findings demonstrate that both temperature and pressure exert a destabilizing effect on silk fibroin, with silk I exhibiting a higher susceptibility to destabilization compared to silk II. Additionally, pressure elevated the van der Waals energy in silk I, while temperature led to a reduction. In contrast, electrostatic potential energy remained unaffected by these environmental conditions, highlighting stable long-range interactions throughout the study. Silk II's tightly packed β-sheet structure offers greater resilience to environmental changes, while the more flexible α-helices in silk I make it more susceptible to structural perturbations. These findings provide valuable insights into the atomic-level behavior of silk fibroin, contributing to a deeper understanding of its potential for applications in environments where mechanical or thermal stress is a factor. The study underscores the importance of computational approaches in exploring protein stability and supports the continued development of silk fibroin for biomedical and engineering applications.

Progress in Multiscale Modeling of Silk Materials

As a result of their hierarchical structure and biological processing, silk fibers rank among nature's most remarkable materials. The biocompatibility of silk-based materials and the exceptional mechanical properties of certain fibers has inspired the use of silk in numerous technical and medical applications. In recent years, computational modeling has clarified the relationship between the molecular architecture and emergent properties of silk fibers and has demonstrated predictive power in studies on novel biomaterials. Here, we review advances in modeling the structure and properties of natural and synthetic silk-based materials, from early structural studies of silkworm cocoon fibers to cutting-edge atomistic simulations of spider silk nanofibrils and the recent use of machine learning models. We explore applications of modeling across length scales: from quantum mechanical studies on model peptides, to atomistic and coarse-grained molecular dynamics simulations of silk proteins, to finite element analysis of spider webs. As computational power and algorithmic efficiency continue to advance, we expect multiscale modeling to become an indispensable tool for understanding nature's most impressive fibers and developing bioinspired functional materials.

Molecular organization of fibroin heavy chain and mechanism of fibre formation in Bombyx mori

Fibroins' transition from liquid to solid is fundamental to spinning and underpins the impressive native properties of silk. Herein, we establish a fibroin heavy chain fold for the Silk-I polymorph, which could be relevant for other similar proteins, and explains mechanistically the liquid-to-solid transition of this silk, driven by pH reduction and flow stress. Combining spectroscopy and modelling we propose that the liquid Silk-I fibroin heavy chain (FibH) from the silkworm, Bombyx mori, adopts a newly reported β-solenoid structure. Similarly, using rheology we propose that FibH N-terminal domain (NTD) templates reversible higher-order oligomerization driven by pH reduction. Our integrated approach bridges the gap in understanding FibH structure and provides insight into the spatial and temporal hierarchical self-assembly across length scales. Our findings elucidate the complex rheological behaviour of Silk-I, solutions and gels, and the observed liquid crystalline textures within the silk gland. We also find that the NTD undergoes hydrolysis during standard regeneration, explaining key differences between native and regenerated silk feedstocks. In general, in this study we emphasize the unique characteristics of native and native-like silks, offering a fresh perspective on our fundamental understanding of silk-fibre production and applications.

An atomistic scale simulation study of structural properties in the silk-fibrohexamerin complex

The use of Bombyx mori silk fibroin in composite materials has been extensively explored in many studies, owing to its remarkable mechanical properties. Recently, the N-glycan-engineered P25 protein was utilized to improve the mechanical properties of silk. However, the mechanism by which N-glycan-engineered P25 protein enhances the mechanical properties of silk remains unclear. This study analyzed the interaction between the P25 protein and silkworm silk using quantum mechanics/molecular mechanics multiscale simulations and discovered stronger hydrogen bonding between the amorphous domain and the P25 protein. The results confirmed that glycoengineering of the mannose molecule in N-glycan in orders of three, five, and seven increased the hydrogen bonding of the amorphous structures. However, P25 has fewer binding interactions with the crystalline domain. Silk amino acids and mannose molecules were analyzed using QM simulations, and hydroxyl and charged amino acids in the amorphous domains were found to have relatively higher reactivity with mannose molecules in N-glycans than basic and aliphatic amino acids in the crystalline domain. This study demonstrates how the N-glycan-engineered P25 protein can improve the mechanical properties of silk fibroin and identifies a key factor for N-glycan-engineered proteins.

Comprehensive advances in the synthesis, fluorescence mechanism and multifunctional applications of red-emitting carbon nanomaterials

Red emitting fluorescent carbon nanomaterials have drawn significant scientific interest in recent years due to their high quantum yield, water-dispersibility, photostability, biocompatibility, ease of surface functionalization, low cost and eco-friendliness. The red emissive characteristics of fluorescent carbon nanomaterials generally depend on the carbon source, reaction time, synthetic approach/methodology, surface functional groups, average size, and other reaction environments, which directly or indirectly help to achieve red emission. The importance of several factors to achieve red fluorescent carbon nanomaterials is highlighted in this review. Numerous plausible theories have been explained in detail to understand the origin of red fluorescence and tunable emission in these carbon-based nanostructures. The above advantages and fluorescence in the red region make them a potential candidate for multifunctional applications in various current fields. Therefore, this review focused on the recent advances in the synthesis approach, mechanism of fluorescence, and electronic and optical properties of red-emitting fluorescent carbon nanomaterials. This review also explains the several innovative applications of red-emitting fluorescent carbon nanomaterials such as biomedicine, light-emitting devices, sensing, photocatalysis, energy, anticounterfeiting, fluorescent silk, artificial photosynthesis, etc. It is hoped that by choosing appropriate methods, the present review can inspire and guide future research on the design of red emissive fluorescent carbon nanomaterials for potential advancements in multifunctional applications.

Engineering Natural and Recombinant Silks for Sustainable Biodevices

Silk fibroin (SF) is a structural protein derived from natural silkworm silks. Materials fabricated based on SF usually inherit extraordinary physical and biological properties, including high mechanical strength, toughness, optical transparency, tailorable biodegradability, and biocompatibility. Therefore, SF has attracted interest in the development of sustainable biodevices, especially for emergent bio-electronic technologies. To expand the function of current silk devices, the SF characteristic sequence has been used to synthesize recombinant silk proteins that benefit from SF and other functional peptides, such as stimuli-responsive elastin peptides. In addition to genetic engineering methods, innovated chemistry modification approaches and improved material processing techniques have also been developed for fabricating advanced silk materials with tailored chemical features and nanostructures. Herein, this review summarizes various methods to synthesize functional silk-based materials from different perspectives. This review also highlights the recent advances in the applications of natural and recombinant silks in tissue regeneration, soft robotics, and biosensors, using B. mori SF and silk-elastin-like proteins (SELPs) as examples.