Amyloids are ordered protein aggregates, found in all kingdoms of life, and are involved in aggregation diseases as well as in physiological activities. In microbes, functional amyloids are often key virulence determinants, yet the structural basis for their activity remains elusive. We determined the fibril structure and function of the highly toxic, 22-residue phenol-soluble modulin α3 (PSMα3) peptide secreted by Staphylococcus aureus PSMα3 formed elongated fibrils that shared the morphological and tinctorial characteristics of canonical cross-β eukaryotic amyloids. However, the crystal structure of full-length PSMα3, solved de novo at 1.45 angstrom resolution, revealed a distinctive "cross-α" amyloid-like architecture, in which amphipathic α helices stacked perpendicular to the fibril axis into tight self-associating sheets. The cross-α fibrillation of PSMα3 facilitated cytotoxicity, suggesting that this assembly mode underlies function in S. aureus.

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The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril

Agarose is a polysaccharide obtained from some seaweeds, with a quite particular structure that allows spontaneous gelation. Agarose-based beads are highly porous, mechanically resistant, chemically and physically inert, and sharply hydrophilic. These features—that could be further improved by means of covalent cross-linking—render them particularly suitable for enzyme immobilization with a wide range of derivatization methods taking advantage of chemical modification of a fraction of the polymer hydroxyls. The main properties of the polymer are described here, followed by a review of cross-linking and derivatization methods. Some recent, innovative procedures to optimize the catalytic activity and operational stability of the obtained preparations are also described, together with multi-enzyme immobilized systems and the main guidelines to exploit their performances.

https://www.mdpi.com/1420-3049/21/11/1577/pdf

Agarose and Its Derivatives as Supports for Enzyme Immobilization

Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88-90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Ca-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have < 6 A° root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction.

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Eperisone hydrochloride (EH) is widely used as a muscle relaxant for patients with muscular contracture, low back pain, or spasticity. Human serum albumin (HSA) is a highly soluble negatively charged, endogenous and abundant plasma protein ascribed with the ligand binding and transport properties. The current study was undertaken to explore the interaction between EH and the serum transport protein, HSA. Study of the interaction between HSA and EH was carried by UV−vis, fluorescence quenching, circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, Forster’s resonance energy transfer, isothermal titration calorimetry and differential scanning calorimetry. Tryptophan fluorescence intensity of HSA was strongly quenched by EH. The binding constants (Kb) were obtained by fluorescence quenching, and results show that the HSA–EH interaction revealed a static mode of quenching with binding constant Kb ≈ 104 reflecting high affinity of EH for HSA. The negative ΔG° value for binding indicated that...

Biophysical Study on the Interaction between Eperisone Hydrochloride and Human Serum Albumin Using Spectroscopic, Calorimetric, and Molecular Docking Analyses.

Self-assembling peptide (SAP) RADA16-I (Ac-(RADA)4-CONH2) has been suffering from a main drawback associated with low pH, which damages cells and host tissues upon direct exposure. In this study, we presented a strategy to prepare nanofiber hydrogels from two designer SAPs at neutral pH. RADA16-I was appended with functional motifs containing cell adhesion peptide RGD and neurite outgrowth peptide IKVAV. The two SAPs were specially designed to have opposite net charges at neutral pH, the combination of which created a nanofiber hydrogel (-IKVAV/-RGD) characterized by significantly higher G′ than G″ in a viscoelasticity examination. Circular dichroism, Fourier transform infrared spectroscopy, and Raman measurements were performed to investigate the secondary structure of the designer SAPs, indicating that both the hydrophobic/hydrophilic properties and electrostatic interactions of the functional motifs play an important role in the self-assembling behavior of the designer SAPs. The neural progenitor cells...

Functional Self-Assembling Peptide Nanofiber Hydrogels Designed for Nerve Degeneration

Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d.

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure.

Efficient classification of Escherichia coli and Shigella using FT-IR spectroscopy and multivariate analysis.

Photonic disinfection, particularly near-infrared (NIR) light triggered antibacterial, has emerged as a highly promising solution for combating pathogenic microbes due to its spatiotemporal operability, safety, and low cost of apparatus. However, it remains challenging to construct NIR-responsive antibacterial agents with high light-converting efficacy and elucidate synergistic mechanisms. In this work, novel ultrathin two-dimensional (2D) BiOCl-Bi2S3-Cu2S ternary heterostructures that can efficiently kill drug-resistant bacteria were synthesized by doping 0D Bi2S3 and Cu2S nanoparticles in the 2D BiOCl nanosheets via a facile one-pot hydrothermal method. Notably, the incorporation of Cu2S nanoparticles bestows strong NIR light-harvesting capability to the composite nanosheets due to their localized surface plasmon resonance (LSPR). Upon NIR light illumination, the BiOCl-Bi2S3-Cu2S nanosheets can exert both enhanced photonic hyperthermia and reaction oxygen species (ROS) generation, serving as single light-activated bi-functional photothermal and photodynamic therapeutics. Here, high-speed hot electrons and large local electronic fields caused by LSPR might play important roles on thermal vibrations and effective carrier separations respectively. Benefiting from the unique ternary heterostructures, both the photothermal conversion efficacy and ROS generation efficacy of BiOCl-Bi2S3-Cu2S nanosheets are remarkably improved in comparison to the binary BiOCl-Cu2S or BiOCl-Bi2S3 nanosheets. Accordingly, the ternary composite nanosheets can effectively kill bacteria via the NIR-driven photonic disinfection mechanism. This work presents a new type of 2D composite nanosheets with ternary heterostructures for NIR photonic disinfection.

Shouning Yang

Papers

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure.

Efficient classification of Escherichia coli and Shigella using FT-IR spectroscopy and multivariate analysis.

Ultrathin Two-Dimensional BiOCl-Bi2S3-Cu2S Ternary Heterostructures with Enhanced LSPR effect for NIR Photonic Bacterial Disinfection.

Heterojunction structured BiOCl-Bi2S3 nanosheets as mitochondria-targeted near-infrared photothermal and photodynamic therapy agent.