Shaoning Yu

Bio: Shaoning Yu is an academic researcher from Fudan University. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 1, co-authored 1 publications receiving 2241 citations.

Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures

Abstract: Infrared spectroscopy is one of the oldest and well established experimental techniques for the analysis of secondary structure of polypeptides and proteins. It is convenient, non-destructive, requires less sample preparation, and can be used under a wide variety of conditions. This review introduces the recent developments in Fourier transform infrared (FTIR) spectroscopy technique and its applications to protein structural studies. The experimental skills, data analysis, and correlations between the FTIR spectroscopic bands and protein secondary structure components are discussed. The applications of FTIR to the secondary structure analysis, conformational changes, structural dynamics and stability studies of proteins are also discussed.

Ultrasensitive Analysis of Exosomes Using a 3D Self-Assembled Nanostructured SiO2 Microfluidic Chip.

Abstract: Conventional microfluidics with a solid mixer for exosome detection is constrained by the low binding efficiency of the solid-liquid boundary effects and reduced sensitivity of individual markers. Here, we report a 3D-SiO2 porous chip that combines nanoscale porous characteristics and multiple exosome specific markers to greatly improve the sensitivity for biosensing. The lower limit of detection was 220 particles/μL exosomes in PBS. We applied the 3D-SiO2 porous chip for prostate cancer (PCa) staging in mice and early detection of clinical PCa patients. The developed method could significantly differentiate the different stages of PCa in mice and improve the early detection rate in clinical patients. Expression of multiple specific markers in clinical serum samples identified disease fingerprints, alongside histological results, which supports the potential application of exosomes as a noninvasive surrogate biopsy for PCa.

Highly efficient synergistic biocatalysis driven by stably loaded enzymes within hierarchically porous iron/cobalt metal-organic framework via biomimetic mineralization.

Abstract: The integration of multimodal chemo-/bio-catalysis for efficient cascade reactions has long provided broad prospects in the field of biotechnology for ages. In this work, we describe the synthesis of a biomimetic multienzyme hybrid with hierarchically porous structure and outstanding catalytic activity via in situ encapsulation of natural enzymes in an iron-cobalt bimetallic metal-organic framework (Fe/Co-MOF, FCM). The combination of a single enzyme (glucose oxidase) or dual enzyme (β-galactosidase and glucose oxidase) with FCM resulted in remarkable synergistic biocatalysis ability; in contrast to simple biocatalyst mixtures in solution, the prepared multienzyme hybrid resulted in 3.2-fold and 2.1-fold improvements in activity for tandem reactions, respectively. The reinforced cascade bioactivity of the multienzyme hybrid benefitted from the synergistic effect between iron/cobalt in the FCM nanozyme, the opened substrate channel between enzymes/nanozymes, and the beneficial effect provided by the hierarchical MOF pores. The enlarged pores not only provided adequate space for immobilized proteins to diffuse and reorientate in FCM with low surface energy, but also reduced the intrinsic mass transfer obstacle to increase the diffusional efficiency of reactants/intermediates. In addition, on account of the shielding effect provided by FCM, the multienzyme hybrid exhibited enhanced tolerance towards severe circumstances and excellent reusability and has been successfully applied in small molecule detection, such as glucose and lactose. The current study highlights the superiority of synergistic bioreactors integrated with the MOF nanozyme and natural enzymes, suggesting great potential for applications in sustainable biomimetic catalysis.

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

Abstract: 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.

Raman spectroscopy of proteins: a review

Abstract: In this work, 26 proteins of different structure, function and properties are investigated by Raman spectroscopy with 488, 532 and 1064 nm laser lines. The excitation lines were chosen in NIR and Vis range as the most common and to show the difference due to normal and resonance effect, sometimes accompanied by the fluorescence. The selected proteins were divided, according to the Structural Classification of Proteins, into four classes according to their secondary structure, i.e. α-helical (α), β-sheet (β), mixed structures (α/β, α + β, s) and others. For all compounds, FT-Raman and two Vis spectra are presented along with the detailed band assignment. To the best of our knowledge, this is the first review showing the potential of Raman spectroscopy for the measurement and analysis of such a large collection of individual proteins. This work can serve as a comprehensive vibrational spectra library, based on our and previous Raman measurements. Copyright © 2013 John Wiley & Sons, Ltd.

Fourier transform infrared spectroscopy

Abstract: Fourier Transform Infrared Spectroscopy: Applications to Chemical Systems Vol 1 Edited by J R Ferraro and L J Basile Pp 311 (Academic: New York, San Francisco and London, 1978) $25; £1625

Biosynthesis of silver nanoparticles using Ocimum sanctum (Tulsi) leaf extract and screening its antimicrobial activity

Abstract: Development of green nanotechnology is generating interest of researchers toward ecofriendly biosynthesis of nanoparticles. In this study, biosynthesis of stable silver nanoparticles was done using Tulsi (Ocimum sanctum) leaf extract. These biosynthesized nanoparticles were characterized with the help of UV–vis spectrophotometer, Atomic Absorption Spectroscopy (AAS), Dynamic light scattering (DLS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Transmission electron microscopy (TEM). Stability of bioreduced silver nanoparticles was analyzed using UV–vis absorption spectra, and their antimicrobial activity was screened against both gram-negative and gram-positive microorganisms. It was observed that O. sanctum leaf extract can reduce silver ions into silver nanoparticles within 8 min of reaction time. Thus, this method can be used for rapid and ecofriendly biosynthesis of stable silver nanoparticles of size range 4–30 nm possessing antimicrobial activity suggesting their possible application in medical industry.

Mechanosensitive self-replication driven by self-organization.

Abstract: Self-replicating molecules are likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. We report here two self-replicating peptide-derived macrocycles that emerge from a small dynamic combinatorial library and compete for a common feedstock. Replication is driven by nanostructure formation, resulting from the assembly of the peptides into fibers held together by beta sheets. Which of the two replicators becomes dominant is influenced by whether the sample is shaken or stirred. These results establish that mechanical forces can act as a selection pressure in the competition between replicators and can determine the outcome of a covalent synthesis.